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Doi:10.1186/1471-2156-10-88
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(hide) 23andMe/SNPs
1.3x risk of prostate cancer 1.4x risk of prostate cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neighbor, rs1447295. The odds ratio for heterozygotes is estimated to be 1.26 (CI: 1.13 - 1.41)...
more pain [http://blog.23andme.com/2009/08/13/snpwatch-genetic-variation-in-morphine-receptor-may-play-a-part-in-coping-with-social-rejection/] associated with needing more morphine for pain relief after surgery and heightened responses to social rejection. stronger cravings for alcohol; if alcoholic, naltrexone treatment 2x more successful
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
4.4x increased risk of exfoliation glaucoma glaucoma risk likely to actually be based on nearby rs3825942
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This SNP, located in an intron of the LOXL1 gene, was initially reported to be associated with exfoliation glaucoma. However, it was shown in the same study to no longer be significant once two other SNPs, which cause actual changes in the LOXL1 protein, were identified. More specifically, the risk allele rs2165241(T) was found to be associated with glaucoma only because it effectively predicted (with 90% probability) the actual high-risk haplotype consisting of rs1048661(G) and rs3825942(C), as oriented with respect to their entries in dbSNP. However, a meta-analysis published in 2010 concluded that it's likely that SNPs rs1048661 and rs2165241 are not directly implicated in the pathogenesis of glaucoma; only the nearby rs3825942 seemed to be the disease-associated SNP. rs2165241 was sign...
1.4x increased risk for diabetes (and perhaps colon cancer) 1.4x increased risk for type-2 diabetes (and perhaps colon cancer).
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
1.3x increased thyroid cancer risk
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Each A at rs965513 increased the odds of thyroid cancer by 1.75 times. Each T at rs944289 increased the odds of thyroid cancer by 1.37 times. A genoset, Gs137, has also been created in SNPedia to represent the increased risk reported for carriers of both variants. See also: 23andMe blog [PharmGKB:Non-Curated GWAS results: Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. (Initial Sample Size: 192 cases, 37,196 controls; Replication Sample Size: 432 cases, 1,727 controls); (Region: 14q13.3; Reported Gene(s): NKX2-1; Risk Allele: rs944289-T); (p-value= 0.000000002).This variant is associated with Thyroid cancer.] [OMIM:THYROID CARCINOMA, PAPILLARY]
mix of muscle types this genotype indicate somewhat impaired muscles
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
normal 1.6x risk of type-1 diabetes
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rs3129934 is a SNP near the HLA-class II region that may be associated with several autoimmune diseases. In a study of two cohorts (Spanish and American multiple sclerosis patients, each numbering several hundred), rs3129934 was the SNP most associated with increased risk for multiple sclerosis. The odds ratio was 3.3 (CI: 2.3 - 4.9, p = 9 x 10e-11). Seven other SNPs were also identified in this study as associated with increased risk for MS. associated with type-1 diabetes 23andMe uses rs9273363 instead of rs3129934 in its reports on type 1 diabetes risk. This SNP was formerly used as a proxy for rs9272346, with this explanation: 'Note: the 2007 Wellcome Trust paper reported a strong association between type 1 diabetes and the SNP rs9272346. Our quality control process flagged data for rs...
blond hair & blue eyes is 4x more likely
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rs1667394 increases susceptibility to Blond rather than brown hair 4.94 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than brown eyes 29.43 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than green eyes 6.74 times for carriers of the A allele For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:Eye color]
1.45x increased osteoarthritis risk
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rs7639618 is one of several SNPs in the DVWA gene found to be associated with osteoarthritis based on a study of several Japanese patient populations. The allelic odds ratio is 1.45 (CI: 1.27-1.65, p = 2.2 x 10e-8) for the minor allele, which is the (T) allele (in dbSNP orientation). Our results suggest that the effect that DVWA amino acid changes have on tubulin binding is unlikely to influence risk of OA in Caucasians. rs7639618 with knee osteoarthritis with an odds ratio (OR) of 1.29, 95% confidence interval (CI) of 1.15 -1.45 and P of 2.70x10(-5), but not for Europeans [OMIM:OSTEOARTHRITIS SUSCEPTIBILITY 6; OS6]
Magnitude: 2
Frequency: 23.2%
References:10
Frequency: 23.2%
References:10
wet earwax
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rs17822931, also known as c.538G>A or G180R, is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 11 ABCC11 gene. This SNP determines wet vs dry earwax as well as sweat production, it is also associated with lipid secretion. It is commonly (T;T) for asians and (C;C) for europeans and africans. gnxp indicates this SNP influences risk of breast cancer in Japanese women. This does not hold true in Caucasian women, though. reddit discussion [OMIM:ATP-BINDING CASSETTE, SUBFAMILY C, MEMBER 11; ABCC11]
~0.4cm taller 0.4cm taller than average
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nature SNP rs1042725 is associated with height (P = 4E-8) in a study involving over 20,000 individuals. The gene harboring this SNP, HMGA2, is a strong biological candidate for having an influence on height, since rare, severe mutations in this gene are known to alter body size in mice and humans. rs1042725 is estimated to explain approx 0.3% of population variation in height in both adults and children (approx 0.4 cm increased adult height per C allele). rs1042725 is associated with increased height (0.36 cm 95% IC[0.12-0.61] per C allele, P=0.004). in men rs1042725 may explain 3% of height variability [PharmGKB:Non-Curated GWAS Results: A common variant of HMGA2 is associated with adult and childhood height in the general population (Initial Sample Size: 4,921 individuals; Replication S...
Magnitude: 2
Frequency: 42.5%
Repute:Good
References:11
Frequency: 42.5%
Repute:Good
References:11
increased memory performance
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In a Swiss cohort: 'Carriers of KIBRA rs17070145 T allele had 24% better free recall performance 5 min after word presentation (P = 0.000004) and 19% better free recall performance 24 hours after word presentation (P = 0.0008) than did noncarriers.' In a US cohort: 'T allele carriers had significantly better memory scores than non-carriers in the Buschke's Selective Reminding Test (SRT). Performance on another episodic memory task, the Rey Auditory Verbal Learning Test (AVLT), was also significantly different between allele groups.' In another Swiss cohort, with a visual episodic memory task: 'T allele carriers also performed significantly better than did noncarriers in this population.' 'Functional magnetic resonance imaging detected KIBRA allele-dependent differences in hippocampal activ...
Magnitude: 2
Frequency: 46.9%
Repute:Bad
References:4
Frequency: 46.9%
Repute:Bad
References:4
adults likely to be 0.22 BMI units higher
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See rs17782313 for details. Measures of Obesity [GWAS:Obesity (extreme)]
1.28x increased basal cell carcinoma risk
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:66
Frequency: 50.0%
Repute:Bad
References:66
1.3x risk for Myocardial Infarction
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
increased risk for heart disease
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discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...
1.5x increased risk for multiple sclerosis
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The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. blog post giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silenc...
2x risk of severe alcohol withdrawal
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rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048. The rs27072 polymorphism has been shown to be significantly associated with ADHD in clinical samples of Canadian children aged 6 to 16 [Feng et al., 2005] and the significant association was also reported by Ouellet-Morin et al. in a Canadian twin study, 2008 (Am. J. of Medical Genetics Part B, 147B:1442-1449 (2008). The interaction between the dopamine transporter gene and age at onset in relation to tobacco and alcohol use among 19-year-olds. Association of promoter variants of human dopamine transporter gene with schiz...
significantly higher sugar consumption?
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rs5400(T;T) carriers had a significantly higher intake of sugars blog discussion Food Preference
slower AIDS progression
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23andMe blog females with one copy of rs5968255(C) progressed from HIV infection to AIDS more slowly with an average of eight years, nearly four times more than females with no copies or males. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? HIV Progression
least likely to be able to smell asparagus metabolites in urine
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Asparagus anosmia research was performed by 23andMe and presented at the 2009 ASHG according to geneticfuture. Asparagus anosmia Asparagus Metabolite Detection [GWAS:Common traits (Other)]
~1.5x increased risk for chronic lymphocytic leukemia
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rs872071 is a SNP associated with the interferon regulatory factor 4 IRF4 gene. In a GWAS study including over 1,500 Caucasian patients with chronic lymphocytic leukemia (CLL), the rs872071(G) allele showed the strongest association (p = 1.91 x 10e-20) of all SNPs studied. The reported odds ratio was 1.54. See also: 23andMe blog A subsequent study () has found a similar association extending to another 800+ Spanish and Swedish CLL patients. rs872071 was also seen to be associated with CLL in Hong Kong Chinese (71 patients), with a reported odds ratio of 1.78 (CI: 1.25-2.53). A related hematologic malignancy, Hodgkin's lymphoma, may also be influenced by rs872071. Two case-control series totalling 529 and 2192 patients found an odds ratio of 1.21 (CI: 1.05-1.39, p = 0.009). [PharmGKB:Non-C...
Magnitude: 1.2
Frequency: 2.7%
References:3
Frequency: 2.7%
References:3
~15-20% lower risk for hypertension or cardiovascular events
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rs13333226 is a SNP in the 5' region of uromodulin UMOD gene. A large GWAS study ultimately totaling over 20,000 cases and almost as many controls concluded that, compared to the far more common allele, the rarer rs13333226(G) allele is associated with a (slightly) lower risk of hypertension (odds ratio 0.87, CI: 0.84-0.91) as well as a 7.7% reduction per allele for risk of cardiovascular events after adjusting for age, sex, BMI, and smoking status (hazard ratio?0.923, CI: 0.860-0.991; p?=?0.027). High Blood Pressure (Hypertension) Kidney Disease
>1.9x risk for restless legs syndrome
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This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ratio of 0.57 (CI: 0.48-0.68). Note that 70-80% of all individuals in European populations carry one or two copies of the (A) major allele, yet restless le...
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Further noteworthy novel findings were observed between SNPs in ESR1 with testosterone levels (rs722208, mean difference = 8.8%, P = 7.37 x 10–6) and SRD5A2 with 3-androstanediol-glucuronide (rs2208532, mean difference = 11.8%, P = 1.82 x 10–6). Sex Hormone Regulation
Frequency: 8.8%
References:0
References:0
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Persistant Fetal Hemoglobin
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
1.4x higher risk for spondylitis
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rs30187 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. Each T allele appears to increase the odds by about 1.4x (p=3.4x10e-10). A study of 872 Korean patients found that each T allele was associated with 1.5x higher odds of ankylosing spondylitis. [GWAS:None]
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23andMe blog *Each G at rs2856683 increases the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. Primary Biliary Cirrhosis: Preliminary Research [OMIM:?]
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Height
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This SNP may be related to longevity. One study found that Ashkenazi who lived to age 95 or older are more likely to have two copies of the C allele.
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Atopic Dermatitis
Frequency: 18.6%
References:0
References:0
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Asthma
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related to Paget’s disease of bone 23andMe blog. [OMIM:?] [GWAS:Paget's disease]
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23andMe blog chronic lymphocytic leukemia *rs735665 A 1.45 news Slager and colleagues validated these in an independent sample of patients. The strongest association was for rs735665 on 11q24, where the risk was 50 percent higher. This was closely followed by a 39 percent increased risk associated with rs9378805 on 6p25. Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma. Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs735665-A). This variant is associated with Chronic ...
likely (slight?) increased risk for Parkinson's disease
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rs9652490 is a SNP in the LINGO1 gene. Note: it is unclear why one set of authors report the risk allele for essential tremors to be (G), while the others just as clearly report the risk allele to be (A). A follow-up case-control study replicated the original association of rs9652490(A;A) to an ~2x increased risk for Parkinson's disease, but also found the same risk for essential tremor (ET), thus linking the two diseases. The ET study was based on ~300 patients. 23andMe blog 'In a combined analysis of 752 subjects with essential tremor from Iceland, Austria, Germany and the United States and 15,797 controls, Stefansson et al found that the G version of rs9652490 in the LINGO1 gene is associated with increased odds of the condition. Carrying one G increases the odds of essential tremor by ...
higher risk for dyslexia
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The more common allele of rs761100 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02. Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impairment. Developmental Dyslexia
normal
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Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs3751812, although this SNP is one of the co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied FTO SNPs, rs9930506 or rs9939609. 23andMe considers rs3751812(T) equivalent to the rs9939609(A) implicated for african americans
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related to Paget’s disease of bone 23andMe blog. [OMIM:?] [GWAS:Paget's disease]
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
None
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rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder Tourette's Syndrome
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Each A allele at rs7743761 is associated with 4.6x higher risk of ankylosing spondylitis, according to a 2007 publication. [GWAS:Ankylosing spondylitis]
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An association between freckling and rs2153271 [GWAS:Freckling]
Frequency: 31.0%
References:9
References:9
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associated with hair color rs12896399 rs12203592 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER] [GWAS:Black vs. blond hair color]
2x risk
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Linked to bipolar disorder in one of the most comprehensive studies in 2007. Risk allele with reference to dbSNP orientation is reported to be (T), with either one or two copies leading to an odds ratio of 2 (CI 1.6-2.7). Some replications, but in 2011 23andMe published as failed to replicate in Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample...
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Brain Aneurysm
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'''rs2269726''' is located in intron 5 within the GNB1L gene on chromosome 22q11. In males, the homozygous genotype, irrespective of whether it is the ancestral (C) or derived (T) allele, is associated with higher risk for schizophrenia than the heterozygous. A 2008 paper showed the association (P = 1.8 × 10-5 (significant in this study); OR = 1.46) in a candidate gene study using a combined German-British sample of 1,408 cases and 2,746 controls. Previous evidence linking GNB1L to schizophrenia includes higher incidence of schizophrenia among those with 22q11 deletions and genetic linkage studies. A well-documented ~3 Mb deletion on chromosome 22q11 is characteristic among those with a variety of psychiatric disorders—together termed 22q11 deletion syndrome (22q11DS)—including Velo-Cardio...
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 6p21.32; Reported Gene(s): BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1; Risk Allele: rs2395185-?); (p-value= 0.0000000000000001).This variant is associated with Ulcerative colitis.] [OMIM:?] [GWAS:Ulcerative colitis]
~2x higher risk for hyperuracemia
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This is basically a surrogate for rs7442295, and thus associated with higher serum urate levels. [OMIM:SOLUTE CARRIER FAMILY 2 (FACILITATED GLUCOSE TRANSPORTER), MEMBER]
normal
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23andMe blog rs8034191(C;C) decreased response to alcohol rs8034191 increases susceptibility to Lung cancer 1.27 times for heterozygotes (CT) and 1.80 times for homozygotes (CC) rs8034191 increases susceptibility to Lung cancer 1.28 times for heterozygotes (CT) and 1.81 times for homozygotes (CC) [PharmGKB:Non-Curated GWAS results: Familial Aggregation of Common Sequence Variants on 15q24-25.1 in Lung Cancer. (Initial Sample Size: 194 cases, 219 controls; Replication Sample Size: 3,878 cases, 4,831 controls); (Region: 15q25.1; Reported Gene(s): LOC123688, PSMA4, CHRNA3, CHRNA5, CHRNB4; Risk Allele: rs8034191-G); (p-value= 0.00000001).This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 2; LNCR2] [GWAS:Lung cancer] [GWAS:Lung cancer]
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news the presence of the G allele was protective against follicular lymphoma, while the presence of the A allele was predictive of an increased risk of developing follicular lymphoma. Dr. Brown said individuals who had the A variant were nearly twice as likely to develop follicular lymphoma. 23andMe blog coverage [OMIM:?] [GWAS:Follicular lymphoma]
1.2x increased risk for chronic kidney disease
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rs6495446, an intronic SNP in the MTHFS gene, was associated with increased risk for chronic kidney disease based on a study associated with the Framingham Heart Study of ~1,000 Caucasian individuals. The odds ratio rs6495446(C) allele was 1.24 (CI: 1.09-1.41, p=0.001).news 23andMe reports this same information with a different emphasis: each T allele lowers the odds of chronic kidney disease by 0.8 times.
can digest milk
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Also known as 'C/T(-13910)', and located in the MCM6 gene but with influence on the lactase LCT gene, rs4988235 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European Caucasian populations. , In these populations, the rs4988235(T) allele is both the more common allele and the one associated with lactase persistence; individuals who are rs4988235(C;C) are likely to be lactose intolerant. In populations of sub-Saharan Africans, though, the rs4988235(T) allele is so rare that it's unlikely to be predictive of lactase persistence, and other SNPs are predictive instead. * See also OMIM 601806.0001 Measuring European population stratification with microarray genotype data. Adult-type hypolactasia is no...
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rs3018362 increases susceptibility to Osteoporotic fractures for carriers of the A allele related to Paget’s disease of bone 23andMe blog. [OMIM:?] [GWAS:Paget's disease]
Frequency: 36.9%
References:6
References:6
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23andMe blog chronic lymphocytic leukemia *rs13397985 G 1.41 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs13397985-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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Associated with increased risk for Crohn's disease in a study of 380 Korean patients. This SNP is associated with greater susceptibility to leprosy in Asians, according to the 23andMe blog. The risk allele is T, and the odds ratio is 1.37. The TNFSF15 gene encodes a cytokine protein in the tumor necrosis factor (TNF) family. TNFSF15 is an ethnic-specific IBD gene. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. TNFSF15 polymorphisms are associated with susceptibility to inflammatory bowel disease in a new European cohort. IBD-associated TL1A gene (TNFSF15) haplotypes determine increased expression of TL1A protein. Comprehensive linkage and association analyses identify haplotype, near to the TNFSF15 gene, significantly associated with spondyloarthrit...
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23andMe blog *Each G at rs2856683 increased the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. [PharmGKB:Curated A GWAS of 2072 Canadian and U.S. subjects (536 patients with primary biliary cirrhosis and 1536 controls) showed that primary biliary cirrhosis was significantly and reproducibly associated with this SNP (rs6441286) at the IL12A locus (P=2.42x10(-14); odds ratio, 1.54).] [OMIM:?] [GWAS:Primary biliary cirrhosis]
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23andMe blog associated rs7927894(T) with Crohn’s disease 1.16x and atopic dermatitis [PharmGKB:Non-Curated GWAS results: A common variant on chromosome 11q13 is associated with Dermatitis, Atopic. (Initial Sample Size: 939 cases, 975 controls, 1,097 family members; Replication Sample Size: 2,637 cases, 3,957 controls); (Region: 11q13.5; Reported Gene(s): C11orf30; Risk Allele: rs7927894-A); (p-value= 0.0000000008).This variant is associated with Dermatitis, Atopic.] [OMIM:?] [GWAS:Atopic dermatitis]
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23andMe blog chronic lymphocytic leukemia *rs7176508 A 1.37 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs7176508-A). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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Brain Aneurysm
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rs1801260, a SNP in the CLOCK gene known as 3111 T/C, has been reported to influence sleep and activity patterns in patients affected by bipolar depression. From this article's abstract: 'Compared to T/T homozygotes, carriers of the C allele had a similar degree of severity of depression, but showed higher activity levels in the evening, a delayed sleep onset (mean 79 min later), and a reduced amount of sleep during the night (mean 75 min less).' Allele frequencies of T3111C SNP of hClock were significantly different between schizophrenics and controls (chi(2) = 19.738, P < 0.05). Schizophrenics had a significantly higher frequency of the C allele compared with controls (OR = 2.613, 95% CI = 1.693-4.034). (Han Chinese population.) There was a strong, significant association (P < 0.00...
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The C allele of this SNP in the NR1H3 gene is associated with increased (but still low) risk of progressive supranuclear palsy. [PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. (Initial Sample Size: 4,763 individuals; Replication Sample Size: NR); (Region: 11p11.2; Reported Gene(s): NR1H3; Risk Allele: rs7120118-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
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Gout (A) increased risk.
higher risk of LDD
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The rs2073711 SNP (1184T→C ) is located in exon 8 of the cartilage intermediate layer protein gene (CILP). However, CILP gene is primarily known to be expressed abundantly in intervertebral discs, and was reported to have increased expression when degeneration occurs . For the rs2073711 SNP, the ancestral allele is T and the disease associated risk allele is C. A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. ==Background== Low back pain (LBP) is an enervating condition that affects 70-85% of all people during their lifetime . It can lead to decreased physical activity and quality of life, presenting considerable negative socioeconomic and health impacts on m...
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DeCode reports that the rs737267(G;T) genotype is associated with 0.77 times the normal risk of gout, and the rs737267(G;G) genotype is associated with 1.25 times higher risk of gout. [PharmGKB:Non-Curated GWAS Results: SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout (Initial Sample Size: 794 individuals; Replication Sample Size: 706 individuals; Risk Allele: rs737267-C).] [OMIM:SOLUTE CARRIER FAMILY 2 (FACILITATED GLUCOSE TRANSPORTER), MEMBER] [GWAS:Serum urate]
4+ IQ points for breastfeeding
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4+ IQ points for breastfeeding with the AA or AG genotypes Breastfeeding and IQ [GWAS:Response to statin therapy]
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Response to Interferon Beta Therapy
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Brain Aneurysm
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rs1892534 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while the rs1892534(A) allele was not likely to be causative (relative to cancer), it is associated with increased risk for cancer overall. The odds ratio for 1 or 2 such alleles was 1.05 (CI: 0.90 - 1.23) and 1.2 (CI: 1.01 - 1.42) overall. Two other CRP SNPs (rs1169300 and rs2464196) were specifically associated with increased lung cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk. [PharmGKB:Curated GWAS Results: Loci Related to Metabo...
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Odor Detection
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rs4693596(C;C) 2x odds of myopathy when taking statins. Statin Response
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-66). Stud...
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Variant in the RIPK2 gene associated with a reduced risk of leprosy in Asians, according to the 23andMe blog. The protective allele is A, and the odds ratio is 0.76. Leprosy Susceptibility [GWAS:Leprosy]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
1.2x increased bladder cancer risk
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rs710521 is a SNP located in chromosome region 3q38, near the TP63 gene. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs710521(A) were at 1.4x increased risk (allele-specific odds ratio = 1.19, p = 1 x 10e-7) for the disease. An additional 1,425 bladder cancer patients, supplemented by a meta-analysis of 5,695 additional cases (and 40,000+ controls), did replicate a (somewhat) increased risk associated with the rs710521(A) allele. The overall odds ratio was 1.18 (OR: 1.12 - 1.25, p < 0.0001). Another study in Chinese populations did not find an increased risk of bladder cancer for this SNP. [PharmGKB:Non-Curated GWAS Results: Sequence variant on 8q24 confers susceptibility to ...
Frequency: 48.7%
References:14
References:14
adult waist 0.9cm larger on average
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A study of 14,000 Indian Asian or Caucasian adults indicates that rs12970134(A) alleles are associated with obesity. The average increase in waist circumference is 0.9cm BMI units per risk allele. see also The common obesity variant near MC4R gene is associated with higher intakes of total energy and dietary fat, weight change and diabetes risk in women. Variants near MC4R are associated with obesity and influence obesity-related quantitative traits in a population of middle-aged people: studies of 14,940 Danes. Investigation of the locus near MC4R with childhood obesity in Americans of European and African ancestry. The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Large effects on body mass index and insulin resistanc...
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may influence age related macular degeneration when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone. age related macular degeneration Age-Related Macular Degeneration [GWAS:Age-related macular degeneration]
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rs2305767 (P = 1.16 x 10(-4); OR 1.41, 95% CI 1.18-1.67). We demonstrate significant association of allelic variants in MYO9B with schizophrenia Crohn's disease rs2305767 associated with inflammatory bowel disease (IBD) overall (corrected P-value 0.002, odds ratio [OR] 0.76, 95% confidence interval [CI] 0.67-0.86)
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rs2976392 and diffuse-type gastric cancer (allele-specific odds ratio (OR) = 1.62, 95% CI = 1.38-1.89, P = 1.11 x 10(-9)). Substitution of the C allele with the risk allele T at a SNP in the first exon (rs2294008, which has r(2) = 0.995, D' = 0.999 with rs2976392) reduces transcriptional activity of an upstream fragment of the gene [OMIM:PROSTATE STEM CELL ANTIGEN; PSCA] [GWAS:Bladder cancer]
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(C;C) greater odds of longevity Replication of an association of variation in the FOXO3A gene with human longevity using both case-control and longitudinal data. Association of the FOXO3A locus with extreme longevity in a southern Italian centenarian study.
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23andMe blog *Each G at rs2856683 increased the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. Vaccine immunogenetics: bedside to bench to population. Replicated association of 17q12-21 with susceptibility of primary biliary cirrhosis in a Japanese cohort. A GWAS follow-up study reveals the association of the IL12RB2 gene with systemic sclerosis in Caucasian populations. Primary Biliary Cirrhosis: Preliminary Research [PharmGKB:Curated A GWAS of 2072 Canadian and U.S. subjects (536 patients with primary biliary cirrhosis and 1536 controls) showed that primary biliary cirrhosis was significantly and reproducibly associated with this SNP ...
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
Frequency: 54.5%
References:5
References:5
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23andMe blog chronic lymphocytic leukemia *rs11083846 A 1.35 [GWAS:Chronic lymphocytic leukemia]
possible increased risk for neuroblastoma
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SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs6939340(G;G) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.97, CI: 1.58 to 2.45, p=9.3 x 10<sup>-15</sup>). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. Presumably driven primarily by the at-risk homozygotes, the rs6939340(G) allele was considered to be a risk factor, however, there was insufficient data to conclude whether rs6939340(A;G) heterozygotes were actually at any increased risk compared to rs6939340(A;A) 'wild-type' homozygotes. ...
1.5x increased risk for asthma
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rs7216389, a SNP in the ORMDL3 gene on chromosome 17q21, was associated with susceptibility to childhood asthma in a study of ~1,000 British patients. The variation appears to be linked to altered levels of the ORMDL3 mRNA, which was shown in a cohort study of ~5,000 British and German patients to be correlated to childhood asthma. A large study of Scottish asthma patients replicated these results, finding that a single copy of the T allele conferred an odds ratio of 1.50 (CI: 1.24-1.81) and 2 copies conferred an odds ratio of 2.11 (CI: 1.71-2.61), respectively. [PharmGKB:Non-Curated GWAS Results: Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma (Initial Sample Size: 994 cases, 1,243 controls; Replication Sample Size: 2,320 cases, 3,301 controls; Ri...
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Variant in the NOD2 gene associated with greater susceptibility to leprosy in Asians, according to the 23andMe blog. The risk allele is C, and the odds ratio is 1.59. Another gene associated with susceptibility to leprosy is TNFSF15. SNPs in both the NOD2 and TNFSF15 genes are also associated with susceptibility to Crohn's disease. Leprosy Susceptibility [GWAS:Leprosy]
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This study compared 608 patients of European ancestry with papillary thyroid cancer, which is the most common form of thyroid cancer and is highly treatable, to 901 healthy controls. The authors found an association between the SNP rs2910164, which is equivalent to the 23andMe SNP rs2961920, and risk for thyroid cancer. People with the AC genotype at rs2961920 had about 1.5 times the odds of papillary thyroid cancer compared to those with the AA genotype and about three times the odds compared to the CC genotype. Though this is an atypical risk pattern, the researchers speculate in a separate paper that having one copy of each form of the SNP increases production of molecules that regulate the cell's response to DNA damage, a process that is often involved in cancer.
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Variant in the C13orf31 region associated with increased susceptibility to leprosy, according to the 23andMe blog 23andMe blog. The risk allele is G, and the odds ratio is 1.68. Other genes associated with both Crohn's disease and leprosy include NOD2 and TNFSF15, according to 23andMe's blog. Leprosy Susceptibility [PharmGKB:Non-Curated GWAS Results: Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease (Initial Sample Size: 3,230 cases 4,829 controls; Replication Sample Size: 2,325 cases 1,809 controls 1,339 affected trios; Risk Allele: rs3764147-G).] [OMIM:?] [GWAS:Leprosy] [GWAS:Crohn's disease]
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[GWAS:Orofacial clefts]
normal
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omim 131240 In a study of 103 candidate genes for coronary artery disease and associated phenotypes in the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, Pare et al. (2007) found that HDL cholesterol levels were associated with a lysine-to-asparagine substitution at codon 198 (K198N) of the EDN1 gene in a sex-specific manner. The minor allele T (Asn) of the K198N substitution (dbSNP rs5370) was associated with lower HDL cholesterol values. Women showed a strong association between dbSNP rs5370 and HDL cholesterol (P = 1.3 x 10(-5)), whereas in men no such significant association was identified (P = 0.14). 3x increase in the adjusted odds of being hypertensive of rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, 9CI: 1.02 - 8.19). Afte...
Frequency: 64.2%
References:5
References:5
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23andMe blog chronic lymphocytic leukemia *rs17483466 G 1.39 Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs17483466-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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Each C allele at rs3914132 decreases the likelihood of developing otosclerosis, which can cause hearing loss. [PharmGKB:Non-Curated In a GWAS done in Belgian-Dutch cases and controls (694 of each, split into a discovery and a replication set) and then in a second replication set of 455 French cases and 480 controls, rs3914132 was found to be associated with otosclerosis.] [OMIM:OTOSCLEROSIS; OTSC1] [GWAS:Otosclerosis]
Frequency: 75.7%
References:5
References:5
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rs10484554 was the most highly significant SNP associated with risk for psoriasis in a large US/UK study. Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. New insights into the pathogenesis and genetics of psoriatic arthritis. Genome-wide association studies and the genetic dissection of complex traits. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. Host Genes Important to HIV ...
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Breast Cancer
Duffy-positive This genotype is associated with European populations and southwestern Native American populations.
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rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. (One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.) Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and southwestern Native American populations. rs2814778(G;G) protect against Plasmodium vivax malaria and predicts of white blood cell and neutrophil count 23andMe blog discussion Malaria Resistance (Duffy Antigen) [PharmGKB:Curated A...
References:1
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Male Infertility
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
The (G;G) genotype averages 2.84 PIQ points lower than (A;A) genotype and averages 2.8 PIQ points lower than (A;G) genotype
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in . The (A;A) genotype averaged 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ. rs363050 is in close linkage with rs353016, with r2 = 0.98, such that the rs363050(A) allele typically is linked to the rs353016(T) allele. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP). Measures of Intelligence
normal
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Each A at rs965513 increased the odds of thyroid cancer by 1.75 times. Each C at rs944289 increased the odds of thyroid cancer by 1.37 times. A genoset, Gs137, has also been created in SNPedia to represent the increased risk reported for carriers of both variants. See also: 23andMe blog [PharmGKB:Non-Curated GWAS results: Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. (Initial Sample Size: 192 cases, 37,196 controls; Replication Sample Size: 432 cases, 1,727 controls); (Region: 9q22.33; Reported Gene(s): FOXE1; Risk Allele: rs965513-A); (p-value= 2E-27).This variant is associated with Thyroid cancer.] [OMIM:THYROID CARCINOMA, PAPILLARY]
susceptible to Norovirus infections
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rs601338 is found on chromosome 19 in the alpha(1,2)-fucosyltransferase FUT2 gene. The wild-type rs601338(G) encodes the 'secretor' (Se) allele, while rs601338(A) encodes the 'non-secretor' (se) allele. A study of 115 Swedish adults concluded that rs601338(A;A) homozygotes have genetic immunity to infection by the Norwalk norovirus, a major (and contagious) cause of acute gastroenteritis worldwide among adults. This illness is also known as 'cruise ship gastroenteritis.' Being a non-secretor may have other consequences, such as greater susceptibility to infection by influenza viruses and by some types of bacteria. 23andMe discusses these topics. In some non-Caucasian populations, a different SNP is responsible for non-secretor phenotypes. For example, although the Se allele is absent in Ja...
can taste bitter
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
Magnitude: 0.1
Frequency: 91.8%
Repute:Bad
References:88
Frequency: 91.8%
Repute:Bad
References:88
normal, but higher risk for certain autoimmune diseases
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-1 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal
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rs2653349, also known as G1246A, is a SNP in the HCRTR2 hypocretin-orexin gene. It has been linked primarily to cluster headaches. The more common allele (G) has been linked to increased risk; alternatively, this could be seen as implying that the less common (A) allele reduces cluster headache risk. In the (first) study, 100+ Italian patients were analyzed to reveal that rs2653349(G;G) genotypes were at 5x increased risk for the disorder, compared with (A;G) and (A;A) genotypes. A study of 200+ German patients indicated that (G;G) homozygotes were at 2x increased risk (CI: 1.32-2.92, p = 0.0007) for cluster headaches. A meta-analysis of 3 pooled studies concluded that the rs2653349(G;G) genotype showed a higher disease risk compared to the remaining genotypes (odds ratio 1.69, CI:1.11-2.5...
Magnitude: 0
Frequency: 3.5%
References:29
Frequency: 3.5%
References:29
brown eye color, 80% of the time observed in User:Watson and User:Dichro
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rs12913832 is a SNP near the OCA2 gene that may be functionally linked to blue or brown eye color, due to a lowering of promoter activity of the OCA2 gene. Blue eye color is associated with the rs12913832(G;G) genotype. For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). rs12913832 is also part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, that is found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other racial groups. rs12913832-T (brown eye) homozygotes compared to rs12913832-C (blue eye). correlations with skin,...
normal
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rs6457617 has been reported in a large study to be associated with rheumatoid arthritis. This SNP is reported to be the most statistically significant of many SNPs similarly located in the MHC region. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 2.36 (CI 1.97-2.84), and for homozygotes, 5.21 (CI 4.31-6.30). [GWAS:Rheumatoid arthritis]
Magnitude: 0
Frequency: 29.2%
Repute:Good
References:1
Frequency: 29.2%
Repute:Good
References:1
lowest odds of photic sneeze reflex
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For photic sneeze reflex, we find a novel association with rs10427255 (score 10.9 and an OR of 1.32). We also find a suggestive association with rs11856995 (score 7.13 and OR of 0.78). The C allele appears to be associated with higher odds of photic sneezing. [GWAS:Common traits (Other)]
normal
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
Magnitude: 0
Frequency: 31.9%
References:10
Frequency: 31.9%
References:10
average
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rs10260404, a SNP in the region of the DPP6 gene on chromosome 7, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The overall odds ratio for the risk allele rs10260404(C) is 1.30 (CI: 1.18-1.43, p=0.017). When broken down by genotype, the odds ratios for heterozygotes are 1.20 (CI: 1.06-1.41), and for rs10260404(C;C) homozygotes, 1.60 (CI: 1.32-1.92). A 'C-C' haplotype for this SNP and that of it's neighbor rs10239794 is also highly (statistically; p=10e-9) associated with ALS. However, in an expanded study pooling 4 populations (Irish, Dutch, US, Polish) rs10260404 failed to reach Bonferroni significance. although it did remain significant in the (expanded) Irish-only population. [PharmGKB:Non-Curated GWAS results: Screening...
normal
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rs9642880 is a SNP located in chromosome region 8q24, a region that has been linked to prostate, breast, and colon cancer. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs9642880(T) were at 1.49x increased risk (allele-specific odds ratio = 1.22, p = 9 x 10e-12) for the disease. This SNP was not associated, however, with risk for prostate, breast, or colon cancer. Another study in Chinese populations found similar results in regard to bladder cancer. rs9642880(T;T) estimated risk of developing 1.49 times that of noncarriers. 1,803 urinary bladder cancer cases and 34,336 controls. No association with prostate, colorectal and breast cancers. In contrast to GSTM1 SNPs, the rs9642880(T...
normal
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
better long-term memory?
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rs1799990, also known as Met129Val or M129V, is a SNP in the prion protein PRNP gene. The more common rs1799990(A) allele encodes the Met (methionine). Historically, since 1991 this SNP has been associated with risk for sporadic Creutzfeldt-Jakob disease, with homozygotes of both types apparently at increased risk compared to heterozygotes. More recently, this SNP has been related to long-term memory with (A;A) and (A;G) individuals recalling 17% more words than (G;G) individuals at 24h following learning. A further study of 12 individuals of each of the 3 possible genotypes showed that at both 30 minutes and 24 hour time lags, correlations between retrieval-related brain activity and retrieval success were negative for (G;) homozygotes (the more activity, the worse retrieval success), whi...
common in clinvar
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer * cleft lip and cleft palate * coronary artery disease * depression * hyperhomocysteinemia * migraine * neural tube defects * pre-eclampsia (ges...
normal
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rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women, rs8179176, rs9340799, rs1256065, and rs1256030 were associated with likelihood of developing cognitive impairment. In men, rs728524, rs1255998, and rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke. A study of 702 cases with invasive endometrial cancer concluded that the less common alleles of SNP rs9340799 lowered risk for the disease. The odds ratio was 0.75 (CI: 0.60-0.93) for (A;G) and 0.53 (CI: 0.37-0.77) for (G;G) compared to rs9340799(A;A) individuals. Endometriosis Uterine Fibroids [PharmGKB:Curated SNP is associated...
1.24x increased myocardial infarction risk, 1.29x increased aneurysm risk
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A common variant on chromosome 9p21 affects the risk of myocardial infarction, and is further discussed in this blog post 23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 9q21.3; Reported Gene(s): CDKN2A, CDKN2B; Risk Allele: rs1333040-T); (p-value= 0.0000000001).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 6] [GWAS:Intracranial aneurysm]
normal
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Magnitude: 0
Frequency: 55.8%
References:8
Frequency: 55.8%
References:8
normal risk
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rs10050860 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.71 (p=7.7x10e-9). Association of an ERAP1 ERAP2 haplotype with familial ankylosing spondylitis. Investigating the genetic association between ERAP1 and ankylosing spondylitis. Serum cytokine receptors in ankylosing spondylitis: relationship to inflammatory markers and endoplasmic reticulum aminopeptidase polymorphisms. ERAP1 polymorphisms and haplotypes are associated with ankylosing spondylitis susceptibility and functional severity in a Spanish population. Associations between ERAP1 polymorphisms and ankylosing spondylitis susceptibility: a meta-analysis.
normal
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A genome-wide association study involving 224 cases and 383 controls of Central European origin found that significant association between rs987525 and risk for nonsyndromic cleft lip with or without cleft palate (NSCL/P). The odds ratio for rs987525(A;G) individuals was 2.57 (CI: 2.02-3.26), and for rs987525(A;A), 6.05 (CI: 3.88-9.43). The calculated population attributable fraction for this marker is 0.41, suggesting that this study has identified a major genetic cause for NSCL/P. 23andMe blog article Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Family-based study shows heterogeneity of a susceptibility locus on chromosome 8q24 for nonsyndromic cleft lip and palate. Association between genetic variants of reported c...
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Sex Hormone Regulation [OMIM:SEX HORMONE-BINDING GLOBULIN; SHBG]
common
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune disease r...
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Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs9298506(A) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.28 (CI:1.20-1.38, p=1.0e-06). Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 8q11.23-q12.1; Reported Gene(s): SOX17; Risk Allele: rs9298506-A); (p-value= 0.000000002).This variant is associated with Intracranial aneurysm.] [OMIM:?] [GWAS:Intracranial aneurysm]
common on affy axiom data
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23andMe blog rs1393350 A 1.29 Melanoma rs1393350 increases susceptibility to Blond rather than brown hair 1.29 times for carriers of the A allele rs1393350 increases susceptibility to Blue rather than green eyes 1.52 times for carriers of the A allele rs1393350 increases susceptibility to Skin sensitivity to sun 1.26 times for carriers of the A allele A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Digital quantification of human eye color highlights genetic association of three new loci. [OMIM:TYROSINASE; TYR] [GWAS:Tanning]
A2/A2 bupropion effective
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain , and has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessation success, or finding no such association. A meta-analys...
Magnitude: 0
Frequency: 67.3%
Repute:Good
References:17
Frequency: 67.3%
Repute:Good
References:17
normal
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rs12425791 is one of 2 SNPs found near the NINJ2 gene on chromosome 12 associated with increased risk for both total stroke and ischemic stroke, based on a large study of four cohorts including both blacks and whites. The other (linked) SNP is rs11833579. Results of this 20,000+ person study suggested that each minor (risk) allele at these two SNPs increases the hazard ratio for total stroke about 1.31 (CI: 1.19 - 1.44) and for ischemic stroke by about 1.40 (CI: 1.27 - 1.56). The corresponding population attributable risks were 11 to 13% for total stroke and 14 to 17% for ischemic stroke, which is fairly high for this sort of SNP. Note: a meta-analysis totaling over 8,000 patients did not replicate any association between either rs12425791 or rs11833579 and ischemic (or incident) stroke. ...
normal
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rs1799884, known also as the -30 SNP of the GCK gene, has been associated with type-2 diabetes. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under a recessive model, the odds ratio for rs1799884(A;A) homozygotes is 2.70 (CI: 1.51-4.83, p=0.0008); under an additive model, the odds ratio is 1.34 (CI: 1.07-1.69, p=0.01). For the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). A common haplotype of the glucokinase gene alters fasting glucose and birth weight: association in six studies and population-genetics analyses. Type 2 diabetes TCF...
Magnitude: 0
Frequency: 69.9%
References:5
Frequency: 69.9%
References:5
normal
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23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 8q11.23; Reported Gene(s): SOX17; Risk Allele: rs10958409-A); (p-value= 0.0000000001).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 10] [GWAS:Intracranial aneurysm]
normal
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rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well by the variant OATP1B1 protein encoded by the rs4149056(C) allele include: *Several cholesterol lowering statins, generally leading to reduced inh...
7x less likely to respond to certain antidepressants
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rs2032583 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
normal
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rs3754777 is a SNP in the serine threonine kinase 39 STK39 gene. A study of ~1,000 Amish originally identified rs3754777 and another SNP also in the STK39 gene, rs6749447, as being significantly associated with hypertension. This association was then found to also hold in patient data analyzed from the Framingham Heart Study and the Diabetes Genetics Initiative. On average, each minor allele, in this case rs3754777(A), is associated with 2.0 mmHg higher systolic blood pressure and a 1.0 mm Hg higher diastolic pressure. High Blood Pressure (Hypertension)
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
common risk allele
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Bipolar disorder failed to replicate in [PharmGKB:Non-Curated GWAS Results: A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder (Initial Sample Size: 461 cases, 563 controls; Replication Sample Size: 772 cases, 876 controls; Risk Allele: rs1012053-A).] [GWAS:Bipolar disorder]
normal
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
common in complete genomics
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rs2066844 is a SNP in the NOD2 gene; the SNP is also known as R702W, with the (C) allele encoding the Arg (R) and the (T) allele encoding the Trp (W). rs2066844 is mentioned in as being strongly associated with Crohn's disease No association was found for NOD2/CARD15 SNPs (R702W, G908R) in Chinese patients with inflammatory bowel disease. [OMIM:CROHN DISEASE, SUSCEPTIBILITY TO]
normal
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. The results derived from a study of 78 Italians with atrial fibrillation (AF) and atrial flutter (AFL) agree with previously reported findings from the Icelandic study (), which also found that the rs2200733(T) was associated with AF/AFL disease. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs2200733 was associated with cardioembolic stroke (CES) (odds ratio 1.54, p = 8.05 x 10e-9). rs2200733 even showed association to ischemic stroke that was not classified as cardioembolic stroke. rs2200733 and rs1003...
straighter hair
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hair curl rs17646946 and rs7349332. source genetic future Appearance [GWAS:Common traits (Other)]
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The T allele of rs9888739 is associated with higher risk of systemic lupus erythematosus. NEJM a combined analysis of the 7380 independent samples generated a maximum combined P=2.02x10–26 and an odds ratio of 1.65 for the association between the T allele of rs9888739 and lupus. [PharmGKB:Non-Curated GWAS Results: Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci (Initial Sample Size: 720 cases, 2,337 controls; Replication Sample Size: 1,846 cases, 1,825 controls; Risk Allele: rs9888739-T).] [GWAS:None] [GWAS:Systemic lupus erythematosus in women]
common on affy axiom data
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[http://7thspace.com/headlines/279477/cathepsin_d_snp_associated_with_increased_risk_of_variant_creutzfeldt_jakob_disease.html] 110 Variant Creutzfeldt-Jakob disease (vCJD) patients were tested for the C-T base change. significant excess of the cathepsin D polymorphism TT genotype in the vCJD cohort compared to controls. The TT genotype was found to have a 9.75 fold increase in risk of vCJD compared to the CT genotype and a 10.92 fold increase compared to the CC genotype. The disease was known as 'mad cow' when an outbreak occurred in Britain in the 1990s. The cathepsin D rs17571 polymorphism: effects on CSF tau concentrations in Alzheimer disease. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or co...
more likely to go bald
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23andMe seems to consider each A at rs925391 to have lowered men's odds of baldness by 11x. baldness *lowest P value of 2.1×10-12 for rs10521339 *family based rs938059 shows the lowest P value (4.03×10-6) (table 3) *rs6152 (P=6.66×10-10)
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23andMe blog () rs10994336 or (rs4948418) Each T at this SNP increased the odds of developing bipolar disorder by 1.45 times compared to the CC genotype. [GWAS:None]
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
average
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In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB1*0301 allele. The HLA-DRB1*0301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). From individuals with the most common rs2187668(G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients. rs2187668(A) also tags the tightly linked DQB1*0201 allele, which in turn is linked to DQA1*0501; together, these are known as the DQ2.5 haplotype. This is the most common haplotype associated with celiac diseas...
common on affy axiom data
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Each A allele at rs2303138 in the LNPEP gene is associated with 1.5x higher odds of ankylosing spondylitis, according to a 2007 report.
common in complete genomics
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According to a 2007 report, each G allele at rs7302230 in the CLSTN3 gene is associated with 1.6x higher odds of ankylosing spondylitis.
common in complete genomics
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rs4140564, a SNP on chromosome 1 near the PTGS2 and PLA2G4A genes, has been associated with knee osteoarthritis. A study of 255 British patients, replicated subsequently in ~2,000 UK, Dutch and US patients, found that rs4140564 was associated with knee osteoarthritis in all populations studied with an overall odds ratio = 1.55, CI: 1.30-1.85, p < 6.9 x 10e-7. [PharmGKB:Curated GWAS results: Genome-wide Association Scan Identifies a Prostaglandin-Endoperoxide Synthase 2 Variant Involved in Risk of Knee Osteoarthritis (Initial Sample Size: 357 cases, 285 controls; Replication Sample Size: 1,177 cases, 2,372 controls). This variant is associated with Knee osteoarthritis.] [GWAS:Knee osteoarthritis]
normal
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rs1447295 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1447295 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs1447295(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.22 (CI: 1.06-1.40, p=5.3x10-3) and may account for 5.4% of population attributable risk. The rs1447295] location could be responsible for about seven percent of prostate cancer cases in white men of north European descent. Thus, taken together with rs6983267, these two genetic changes could account for as much as one quarter of prostate cancer cases in white men. The increased risk was observed for all...
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
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rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
common in complete genomics
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*rs6232 G allele (in dbSNP orientation) linked to 1.34x increased risk of obesity *rs6234/rs6235 (or rs10515237) see also: spitoon Obesity: Preliminary Research [PharmGKB:Curated In a study at 13,659 individuals of European ancestry the N221D variant was consistently associated with obesity in adults and children.] [OMIM:PROPROTEIN CONVERTASE, SUBTILISIN/KEXIN-TYPE, 1; PCSK1]
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
common
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DNA-based methods in the immunohematology reference laboratory. Molecular basis of the Kell (K1) phenotype. Non-ABO Blood Groups [OMIM:KELL K/k BLOOD GROUP POLYMORPHISM]
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele gained...
common in clinvar
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gnxp hair thickness for asians gnxp blog tooth shape among asians A picture of shovel shaped incisors is at http://www.flickr.com/photos/39602184@N02/3747590190/ [OMIM:ECTODYSPLASIN A RECEPTOR; EDAR]
normal
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Tests for th...
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Risk of Placental Abruption and Venous Thromboembolism according to 23andMe The publicly-recognized name for this SNP is rs1799963. Oral Contraceptives, HRT and Risk of VTE
not resistant to HIV
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this snp is on the 23andMe microarray but lacks a dbSNP identifier. discussed in the 23andMe blog *II +/+: Not resistant to HIV infection; shows average time of progression to AIDS after infection. *DI Delta32/+: Not resistant to HIV infection but may have slower progression to AIDS after infection. *DD Delta32/Delta32: Resistant to infection by the most common strain of HIV people usually encounter, though protection is not complete. Article also seems to discuss rs333 (aka CCR5Delta32) Resistance to HIV/AIDS
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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In perfect contrast to another SNP also within the LRRK2 gene, rs34637584, this SNP, rs34778348, is not found in Caucasian populations but is found in Asian populations. A case-control study of 989 Chinese subjects concluded that the odds ratio for Parkinson's disease was 2.1 for rs34778348(A) carriers (CI: 1.1-3.9, p = 0.014). This SNP was estimated to account for 4% of all Parkinson cases in this population. 23andMe blog Parkinson's disease [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2] [GWAS:None]
some resistance to tuberculosis
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The SNP rs4804803 is a variant (-336A>G) in the promoter region for the CD209 gene that results in altered CD209 transcription. It is associated with modified resistance to several infectious diseases, including viruses (Hepatitis C, HIV, dengue, SARS), and bacteria (Mycobacterium tuberculosis), as well as other disorders of varying etiology (ulcerative colitis). The CD209 gene encodes a transmembrane receptor found on the surface of dendritic cells and macrophages. The protein product of CD209, DC-SIGN, plays an important role within both the innate and adaptive immune systems. DC-SIGN's role differs depending on which cell type it resides. On macrophages, DC-SIGN is responsible for recognizing and binding to mannose-type carbohydrates, which are found in almost all pathogenic organism...
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rs174575, has been investigated with respect to increased intelligence in breastfed children but not yielded any clear result. *Although there was no difference in IQ linked to the SNP alone, breastfed children carrying one or two copies of rs174575(C) had a significant (6 point) increase in IQ compared to carriers of the same allele who were not breastfed. For children who were homozygous non-carriers, i.e. rs174575(G;G) individuals, there was no effect of breastfeeding on IQ. *did not replicate those findings. In contrast to their study, (G;G) children exhibited the greatest difference between feeding methods such that breastfed children performed similarly irrespective of child genotype whereas formula fed (G;G) children performed worse than other children on formula milk Breastfeeding ...
common
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rs7566605 was initially reported as being associated in at least 4 independent populations as being associated with obesity however replications are inconsistent, and a recent (2009) large meta-analysis comprising 34 studies (and over 70,000 subjects) has concluded that there is no evidence for overall association of the rs7566605 polymorphism with obesity. See also: Poster At least one population has since been reported in which this association was not seen. Furthermore, a study of 18,000 Danish subjects also failed to find any direct role for this SNP in the development of obesity, except that among physically inactive subjects, (C)-allele carriers tended to have a higher body mass index (by O.5 kg/m2) than (G)-allele carriers. On the other hand, a report has also been published indicat...
common in complete genomics
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rs4950928 in CHI3L1 is likely to play roles in the predisposition to schizophrenia. An attempt to repeat the association between rs4950928 and risk for schizophrenia in an ethnically identical population (Japanese) as well as a new population (Han Chinese) failed to show any significant association. In contrast to previous studies, in this study of 6514 Danish adults the rs4950928(G) allele - rather than the (C) allele - was found to be associated with asthma. [PharmGKB:Non-Curated GWAS Results: Effect of Variation in CHI31 on Serum YKL-40 Level, Risk of Asthma, and Lung Function (Initial Sample Size: 632 individuals; Replication Sample Size: 206 children; Risk Allele: rs4950928-G). This variant is associated with YKL-40 levels.] [OMIM:CHITINASE 3-LIKE 1; CHI3L1] [GWAS:YKL-40 levels]
normal
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rs1573496 is a SNP in the ADH7 alcohol dehydrogenase 7 gene. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1573496(G) allele has a protective effect. Carriers of this allele had a 0.68x (decreased; p=10<sup>-9</sup>) risk of having one of these cancer types. A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium. The data in this paper, makes it seem that (G;G) was much more common. This is inconsistent with the HapMap frequencies, suggesting the sequence may have been flipped. Diplotype trend regression analysis of the ADH gene cluster and the ALDH2 gene: multiple significant associations with alcohol dependence. Multiple ADH genes modulat...
normal risk for gallstones
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rs11887534, a SNP in the hepatic cholesterol transporter ABCG8 gene, has been implicated in gallstone disease, a process known formally as cholelithiasis. The common allele, rs11887534(G), encodes the aspartic acid (D), while the minor (C) allele encodes histidine (H). In a study of ~1,000 German patients, the overall odds ratio associated with rs11887534(C) carriers was 2.2 (CI: 1.8-2.6, p=1.4x10<sup>-14</sup>), and for (C;C) homozygotes, 7x. Up to 10% of the population attributable risk for gallstones may be accounted for by this SNP. [PharmGKB:Curated GWAS Results: A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease (Initial Sample Size: 280 cases, 360 controls; Replication Sample Size: 2...
169 snps
(hide) 5-HTTLPR
higher scores on anxiety-related personality traits; greater placebo response One study of 25 people shows this genotype was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. This SNP has been linked to several psychiatric and/or behavioral phenomena, including: *higher scores on anxiety-related personality traits *obsessive compulsive disorder *panic disorder with a possible gender-dependent effect
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rs4570625, also known as G-703T, is a SNP in the tryptophan hydroxylase 2 TPH2 gene. This SNP has been linked to several psychiatric and/or behavioural phenomena, including: * rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder * rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission * rs4570625(G;G) homozygosity was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. g2b2mh is rs4570625(G;G) is a significant predictor of clinical placebo response? maybe not panic disorder with a possible gender-dependent effect Transmission disequilibrium of polymorphic variants in the tryptophan hydroxylase-2 gene in attention-deficit/hyperactivity disorder. Associa...
may be part of a haplotype associated with OCD
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rs25532 is a SNP in a regulatory region upstream of the serotonin transporter SLC6A4 gene. The more common allele, rs25532(C), is the higher-expressing allele. A study of patients with obsessive compulsive disorder (OCD) concluded that the major allele of rs25532 was a major contributor to the association of a corresponding haplotype with this disorder. [PharmGKB:Curated This study found that the minor allele of the functional C > T single nucleotide polymorphism, rs25532, located less than 150 nucleotides centromeric of the serotonin transporter-linked polymorphic region indel (known as 5-HTTLPR) significantly decreased luciferase reporter gene expression levels by 15-80%, depending on 5-HTTLPR allele background and cell type.]
2 snps
(hide) African American
1.4x increased risk for diabetes (and perhaps colon cancer) 1.4x increased risk for type-2 diabetes (and perhaps colon cancer).
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
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This is a triallelic SNP - note that the sidebar (currently) only shows 3 of the 6 possible genotypes. ====CRP==== claims that this SNP does not affect the serum concentration of CRP, while older resources seem to disagree. However, they do report an association between CRP levels and risk of abdominal aortic aneurysm (AAA). rs3091244 serum CRP level and cardiovascular risk in the NHLBI Family Heart Study. the AA genotype of the triallelic SNP rs3091244 in the gene C-reactive protein was associated with prevalent coronary heart disease in the non-Hispanic white population Association study of CRP gene polymorphisms with serum CRP level and cardiovascular risk in the NHLBI Family Heart Study. rs3093059 rs3091244 Weaker linkage disequilibrium in this region in African Americans allows the co...
common one paper reports increased risk of alcoholism for African-Americans with this genotype.
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This paper found significant association with rs2066702, the SNP that defines ADH1B*3, in African American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B*1, and the low-risk allele encodes ADH1B*3. A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.In some African American] and Native American populations, the ADH1B*3 allele (Arg369Cys in exon 9) is correlated with protection against alcoholism. [PharmGKB:In-Depth This allele has been found in some African American and Native American populations to be correlated with prote...
3 snps
(hide) Ageing
Accelerated lung decline in smokers
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs7557067-G); (p-value= 0.000000000009).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
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[GWAS:None]
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Polymorphisms of the DNMT3B gene and risk of squamous cell carcinoma of the head and neck: a case-control study. Haplotypes of DNMT1 and DNMT3B are associated with mutagen sensitivity induced by benzo[a]pyrene diol epoxide among smokers. Human intelligence and polymorphisms in the DNA methyltransferase genes involved in epigenetic marking. Dietary methyl donors, methyl metabolizing enzymes, and epigenetic regulators: diet-gene interactions and promoter CpG island hypermethylation in colorectal cancer. Genetic variation in the promoter of DNMT3B is associated with the risk of colorectal cancer. DNMT3B promoter polymorphisms and risk of late onset Alzheimer's disease. Low-level environmental cadmium exposure is associated with DNA hypomethylation in Argentinean women.
normal
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rs693 increases susceptibility to Elevated Apolipoprotein B and LDL-Cholesterol for carriers of the T allele [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs693-G); (p-value= 0.00000000000000004).This variant is associated with LDL cholesterol.] [OMIM:APOLIPOPROTEIN B; APOB] [GWAS:Cholesterol, total]
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rs2229765(A;A) associated with ischemic stroke (OR = 1.641, P = 0.022) in a Chinese population
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Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Ala55Val polymorphism on UCP2 gene predicts greater weight loss in morbidly obese patients undergoing gastric banding. Lack of association between uncoupling protein-2 Ala55Val polymorphism and incident diabetes in the atherosclerosis risk in communities study. Ser1369Ala variant in sulfonylurea receptor gene ABCC8 is associated with antidiabetic efficacy of gliclazide in Chinese type 2 diabetic patients. Human uncoupling protein 2 and 3 genes are associated with obesity in Japanese. Physiogenomic comparison of edema and BMI in patients receiving ros...
less mental decline with age
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rs3758391, a SNP in the SIRT1 gene, has been reported to potentially have some role in either longevity, or with higher statistical significance, better cognitive function in older individuals. SIRT1 is thought to regulate neuronal metabolism and survival in response to stress, and the equivalent gene in other species influences maximal life span. The study reporting improved cognition for carriers of rs3758391(T) alleles was based on over 1,000 Finnish adults over the age of 85, and a weak trend towards lower cardiovascular disease was also reported for this allele.
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[GWAS:None]
Frequency: 39.8%
References:1
References:1
higher blood pressure if <50
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rs8192678 encodes a SNP also known as Gly482Ser; the (A) allele encodes the Ser. Some reports have linked this SNP to risk for hypertension and systolic blood pressure (SBP). However, a meta-analysis of 13,000+ individuals did not find any such association. However, gene-age interaction was apparent. For diastolic blood pressure (DBP), p(interaction)<0.0001; for systolic BP, p(interaction)=0.026. In younger individuals (<50yrs; n=2511) the rs8192678(A) allele was associated with higher DBP (p=4.2 x 10<sup>-12</sup>) and SBP (p=7.2 x 10<sup>-12</sup>), but no association was evident for individuals over 50yrs (n=5088). Analysis of PGC-1alpha variants Gly482Ser and Thr612Met concerning their PPARgamma2-coactivation function. PPARGC1A coding variation may initiat...
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Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes. Genetic prediction of future type 2 diabetes. Interaction between the UCP2-866G/A, mtDNA 10398G/A and PGC1alpha p.Thr394Thr and p.Gly482Ser polymorphisms in type 2 diabetes susceptibility in North Indian population. Association between obesity and insulin resistance with UCP2-UCP3 gene variants in Spanish children and adolescents. Association of genetic variants with chronic kidney disease in Japanese individuals. Polymorphisms of the UCP2 gene are associated with proliferative diabetic retinopathy in patients with diabetes mellitus. Interaction between the UCP2 -866 G>A polymorphism, diabetes, and beta-blocker use among patients with acute coronary syndromes. Effect of the common -866G/A polymorphism of the u...
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rs1367117 (C711T/711C>T) is a SNP within APOB (Apolipoprotein B). among 97 hypertensive subjects, C allele carriers responded to irbesartan with an average blood pressure reduction of 19 mmHg, however, they did not respond to atenolol associated with apoB levels [PharmGKB:Curated The APOB:711C>T, C allele was associated with reduction of blood pressure in response to irbesartan treatment but not atenolol treatment.] [OMIM:?] [GWAS:None]
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[OMIM:UNCOUPLING PROTEIN 3; UCP3]
Frequency: 58.4%
References:1
References:1
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Associated with risk of lung cancer in a Chinese population Effects of the type 2 diabetes-associated PPARG P12A polymorphism on progression to diabetes and response to troglitazone.
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[GWAS:Lipoprotein-associated phospholipase A2 activity and mass]
References:15
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* rs2279744, rs1042522, rs17878362 and rs1625895 associated with high grade endometrial cancer
References:0
common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-1 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
common in clinvar
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Variations in the peroxisome proliferator-activated receptor-gamma gene and melanoma risk. PPAR-gamma gene polymorphisms and psoriatic arthritis. The Genetics of PPARG and the Skeleton. The association of Pro12Ala polymorphism of peroxisome proliferator-activated receptor-gamma gene with serum osteoprotegerin levels in healthy Korean women. Association of stearoyl-CoA desaturase 1 activity with familial combined hyperlipidemia. Polymorphism of genes related to insulin sensitivity and the risk of biliary tract cancer and biliary stone: a population-based case-control study in Shanghai, China. PPAR Genomics and Pharmacogenomics: Implications for Cardiovascular Disease. Association of FTO with obesity-related traits in the Cebu Longitudinal Health and Nutrition Survey (CLHNS) Cohort. Differen...
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
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[GWAS:Drug-induced liver injury]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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rs17887200 and rs12951053 associated with ER negative breast cancer tumors (1.48 (1.11-1.93) p-trend = 0.01 and 1.29 (1.06-1.58) p-trend = 0.009, respectively)
52 snps
(hide) APOE
Magnitude: 1.5
The two snps necessary for APOE E3 were observed. However due to the lack of phased data, other possibilities may exist. This is the most common genotype, without significantly increased risk of Alzheimer's disease
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This appears to be the snp on the Illumina Human 550 which is closest to rs4420638 [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 19q13.32; Reported Gene(s): TOMM40, APOE; Risk Allele: rs439401-G); (p-value= 0.000000002).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
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obstructive sleep apnea rs405509 Significant Alzheimer's disease associations with were found for rs449647(A;A) and rs405509(G;G) genotypes (positive), and rs449647(A;T) and rs405509(T;T) [PharmGKB:Curated A study in 2150 Japanese individuals with metabolic syndrome, including 411 subjects with chronic kidney disease (CKD) and 1739 controls found that the -219G-->T SNP in APOE (rs405509) was most significantly associated with CKD in Japanese individuals with metabolic syndrome.]
normal
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rs3025786 is a SNP in the presenilin 1 PSEN1 gene. A study of a Spanish case-control sample of 1,183 individuals showed rs3025786 was associated with Alzheimer's disease in an ApoE-specific manner: more specifically rs3025786(C) allele carriers have a decreased AD risk among carriers of the ApoE4 allele.
normal
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rs5963409 is a SNP in the ornithine carbamoyltransferase OTC gene; this SNP is also known as the -389 G/A SNP. Previous association studies were extended to a population of 2113 Alzheimer's disease cases and 1580 controls from northern France, western France, the United Kingdom and Italy. The rs5963409(A) minor allele was weakly but significantly associated with an increased risk of developing Alzheimer's disease (odds ratio 1.19, p = 0.004). This association was independent of age and ApoE status.
normal
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rs440446 is a SNP in an intron of the apolipoprotein E APOE gene; it is also known as the IVS1+69 variant. In a study of ~1,000 Chinese patients with various biliary tract conditions, including cancer and gallstones, men carrying a rs440446(C) allele (in dbSNP orientation) had a 1.7x risk of gallstone disease [CI: 1.2-2.4], a 1.8x risk of gallbladder cancer (CI: 1.0-3.3), a 3.7x risk of bile duct cancer (CI: 2.0-7.0), and a 4x risk of ampullary cancer (CI: 1.4-12.4). Note: orientation relative to dbSNP entry is reversed as published. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Subarachnoid hemorrh...
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Significant Alzheimer's disease associations with were found for rs449647(A;A) and rs405509(G;G) genotypes (positive), and rs449647(A;T) and rs405509(T;T)
Conflicting reports of possible small increase in Alzheimer's risk. Currently dubious at best.
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Conflicting reports of possible small increase in Alzheimer's risk. Currently dubious at best. rs2373115 is one of several SNPs in the GAB2 gene indicating an increased risk (OR 4.1) of late-onset Alzheimer's disease, but apparently only in individuals also carrying ApoE4 alleles, i.e. rs429358(C) alleles rs2373115 marker does not modify the risk of Alzheimer's disease in Spanish APOE e4 carriers. rs2373115(G) is the risk allele. (p = 9 x 10(-11)) was associated with an odds ratio of 4.06 (confidence interval 2.81-14.69) However, a separate study of 1,749 Alzheimer patients concluded that this GAB2 SNP is 'at best a minor genetic determinant' since the authors of this study observed only a slight tendency for an increase of the (G;G) genotype (odds ratio of 1.3 vs (G;T) and (T;T), CI:1.0-1...
normal risk
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
normal
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rs669 is a SNP in the alpha-2-macroglobulin A2M gene. In dbSNP orientation, the rs669(A) allele encodes an isoleucine, and the rs669(G) allele encodes a valine; the SNP is also known as the Ile/Val variant. On its own, rs669 was not seen to reproducibly and independently increase risk for Alzheimer's disease in several studies of ~200 Italian patients. However, the T-C-A haplotype of rs12316150-rs1050283-rs669 was associated with both early- and late-onset Alzheimer's disease. The majority of the disease risk from this haplotype was based on rs1050283. The original 2004 study of 148 Italian sporadic AD patients yielded an odds ratio for the rs669(G;G) genotype (as oriented in dbSNP orientation) of 3.81 (CI: 1.66-8.75). The presence of rs2333227(C;C), in addition to rs669(G;G), appears to s...
Magnitude: 0
Frequency: 98.2%
Repute:Bad
References:18
Frequency: 98.2%
Repute:Bad
References:18
normal Since the rare geno is good, this can be considered slightly bad
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rs11591147, also known as R46L, is a SNP in the PCSK9 gene. As early as 2006, the minor rs11591147(T) allele was reported to be associated with lower LDL cholesterol levels, and most studies since have found that this also correlates to a two to three fold reduced risk for both early- and late-onset cardiovascular events and disease. As part of a 9 SNP set studied in a meta-analysis totaling over 300,000 patients, rs11591147 was the SNP with the greatest effect on LDL-C and therefore cardiovascular risk reduction. The set of SNPs was as follows, ordered from strongest to least effect on coronary risk, and the allele shown is the one associated with reduced LDL-C levels along with the associated (or nearby) lipid metabolism gene: * rs11591147(T), PCSK9 * rs4420638(A), APOE * rs6511720(T), L...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common
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This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an Apo-ε4 allele. The Apo-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between the...
more likely to gain weight if taking olanzapine
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and o...
common in clinvar
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The ancestral allele is C. Association of ApoE genetic variants with obstructive sleep apnea in children. Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes. [OMIM:HYPERLIPOPROTEINEMIA, TYPE III, ASSOCIATED WITH APOE2]
1 genoset 17 snps
(hide) Appearance
probably light-skinned, European ancestry This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.
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This SNP influences skin pigmentation. The allele p.A111T, rs1426654(A), indicates light-skinned european ancestry. It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned. This SNP is one of three from the SLC24A5 gene that can be analyzed to categorize the ancestry of a person as either European, African, or Asian, based on a 2009 study. The 3 SNPs are: * rs1426654 * rs2555364 * rs16960620 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER]
2-4x higher risk of sun sensitivity if part of risk haplotype
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rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
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blog The two most significant associations found were between nose width and SNP rs1258763 near the GREM1 gene in the German cohort (P=6 × 10?4), and between bizygomatic distance and SNP rs987525 at 8q24.21 near the CCDC26 gene (P=0.017) Genetic determination of human facial morphology: links between cleft-lips and normal variation. Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
Frequency: 31.7%
References:4
References:4
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs35264875-T). This variant is associated with Blond vs. brown hair.] [OMIM:TWO-PORE SEGMENT CHANNEL 2; TPCN2] [GWAS:Blond vs. brown hair]
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
Frequency: 40.7%
References:0
References:0
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Influences appearance gnxp
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
2.3x risk of cleft lip
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risk of cleft lip 23andMe considers rs861020 a proxy Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. Current concepts in genetics of nonsyndromic clefts. Studies of palatine rugae and interferon regulatory factor 6 variations in a group of families with sporadic hypodontia. IRF6 gene variants in Central European patients with non-syndromic cleft lip with or without cleft palate. Family-based study sh...
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Influences appearance gnxp For the rs642742 SNP (184745.0002), located 326 kb upstream of the KITLG transcription start site, the frequency of the ancestral A allele is at least 92% in West Africans, whereas the frequency of the derived G allele is at least 86% in Europeans and East Asians. Admixture mapping suggested that replacement of AA with GG in the rs642742 SNP may account for a lightening of a person's skin by 6 to 7 melanin units. In comparison, the overall skin reflectance difference between West Africans and Europeans is 30 melanin units. [OMIM:KIT LIGAND; KITLG]
Frequency: 81.5%
References:0
References:0
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
brown/black eyes more likely
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
common in clinvar
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Influences appearance gnxp [OMIM:TWO-PORE SEGMENT CHANNEL 2; TPCN2]
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
normal
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A genome-wide association study involving 224 cases and 383 controls of Central European origin found that significant association between rs987525 and risk for nonsyndromic cleft lip with or without cleft palate (NSCL/P). The odds ratio for rs987525(A;G) individuals was 2.57 (CI: 2.02-3.26), and for rs987525(A;A), 6.05 (CI: 3.88-9.43). The calculated population attributable fraction for this marker is 0.41, suggesting that this study has identified a major genetic cause for NSCL/P. 23andMe blog article Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Family-based study shows heterogeneity of a susceptibility locus on chromosome 8q24 for nonsyndromic cleft lip and palate. Association between genetic variants of reported c...
Magnitude: 0
Frequency: 70.8%
Repute:Good
References:18
Frequency: 70.8%
Repute:Good
References:18
common on affy axiom data
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plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent associated with hair color rs12896399 rs12203592 rs12203592 for freckling was previously associated with hair color, eye color, and tanning response to sunlight Squamous Cell Carcinoma [PharmGKB:Non-Curated GWAS Results: A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation (Initial Sample Size: 2,287 women; Replication Sample Size: up to 8,465 individuals; Risk/trait Allele: rs12203592-T). This variant is associated with Black vs. red hair color.] [GWAS:Eye color] [GWAS:Black vs. red hair color]
Magnitude: 0
Frequency: 71.7%
References:8
Frequency: 71.7%
References:8
normal
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A 2007 study based on the Icelanders and Dutch concluded that individuals with an rs12821256(C) allele were ~2x fold more likely to have blond than brown hair color. The specific odds ratio claimed is 2.32, p = 5.5 x 10<sup>-14</sup>. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with blond vs. brown hair.] [OMIM:KIT LIGAND; KITLG] [GWAS:Hair color] [GWAS:Blond vs. brown hair]
straighter hair
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hair curl rs17646946 and rs7349332. source genetic future Appearance [GWAS:Common traits (Other)]
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
normal
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Although the rs26722(T) alllele is relatively rare, at least statistically it seems to be associated with darker eye, hair, and skin color, all other things being equal. A genomewide association study of skin pigmentation in a South Asian population. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Association of the SLC45A2 gene with physiological human hair colour variation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Genetic determinants of hair and eye colours in the Scottish and Danish populations. [OMIM:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
generally non-European, but if European, 7x more likely to have black hair
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pi...
28 snps
(hide) Appearance/Eye color
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
Frequency: 40.7%
References:0
References:0
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Influences appearance gnxp
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
brown/black eyes more likely
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
8 snps
(hide) Ashkenazi Jews
1.3x increased risk for type-2 diabetes
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
1.20x risk for breast cancer
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Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: *rs2981579(A) *rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
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rs6584400 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (A) of rs6584400 was found to be associate...
Frequency: 82.3%
References:4
References:4
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rs10748842 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (C) of rs10748842 was found to be associa...
Duffy-positive This genotype is associated with European populations and southwestern Native American populations.
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rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. (One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.) Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and southwestern Native American populations. rs2814778(G;G) protect against Plasmodium vivax malaria and predicts of white blood cell and neutrophil count 23andMe blog discussion Malaria Resistance (Duffy Antigen) [PharmGKB:Curated A...
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rs10883866 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (G) of rs10883866 was found to be associa...
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This SNP has been related to exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: CETP V405 valine homozygosity (GG genotype) is asso...
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i400415, also known as N370S (risk genotype CC) Possibly associated with Gaucher's disease. * Type I (N370S homozygote), the most common, also called the 'non-neuropathic' type occurs mainly in Ashkenazi Jews, at 100 times the occurrence in the general populace. The median age at diagnosis is 28 years of age, and life expectancy is mildly decreased. There are no neurological symptoms. Parkinson's disease Gaucher Disease
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
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According to 23andMe, only the A allele at rs12948217 confers risk to Canavan disease. A person with the CC, CT, or TT alleles is not a carrier; someone with the AC or AT alleles is a carrier; and people with two AA alleles are affected with the disease. [OMIM:[[Canavan disease]]]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs34516635 is one of a small number of (rare) SNPs in the IGF1R gene found in a study of 384 Ashkenazi centenarians to potentially be associated with longevity. The rs34516635(A) allele was found somewhat more frequently (p=0.02) in female centenarians than in controls. No association was found for males. Higher IGF1 levels and an average decrease in maximal lifetime height of 2.5cm were also reported to be associated with (female Ashkenazi) centenarians.
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
common in complete genomics common for Caucasians on the 23andme platform
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also known as rs28933380 related to colorectal cancer, FAMILIAL, Ashkenazi * APC l1307K: Introduction - Johns Hopkins Hereditary Colorectal Cancer Website [OMIM:?]
13 snps
(hide) BCHE
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This SNP, on chromosome 3 upstream of BCHE (butyrylcholinesterase), is associated with higher cerebral amyloid deposition. The risk allele is G. [http://www.nature.com/mp/journal/vaop/ncurrent/fig_tab/mp201319f4.html]
normal
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
Typical BuChE
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rs1799807, also known as D70G, is a SNP in the BCHE gene. This SNP affects the structure, activity, and substrate specificity of the BuChE (butyrylcholinesterase) enzyme. [Cholinesterases and cholinesterase inhibitors, p. 48] The variant form, rs1799807(G), replaces aspartate with glycine at the secondary substrate/inhibitor binding site. This single base substitution yields the 'atypical' version of BChE. This version has a lower affinity for many substrates, including many Cholinesterase Inhibitors (CIs). A different cholinesterase (acetylcholinesterase, AChE) is an important component of neurotransmission by acetylcholine (ACh), terminating the action of ACh after it has been released during neurotransmission. BChE is found widely in the plasma and normally binds to CIs, protecting AChE...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar common
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(T;T) has a moderate change in BCHE activity according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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(T;T) abolishes catalytic activity in BCHE according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 2]
5 snps
(hide) Breast size
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breast size
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[GWAS:Breast size]
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[GWAS:Breast size]
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[GWAS:None]
Frequency: 49.6%
References:1
References:1
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[GWAS:Breast size]
Frequency: 51.3%
References:1
References:1
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[GWAS:Breast size]
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[GWAS:Breast size]
Frequency: 65.5%
References:1
References:1
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breast size
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[GWAS:Breast size]
9 snps
(hide) Cannabis
more pain [http://blog.23andme.com/2009/08/13/snpwatch-genetic-variation-in-morphine-receptor-may-play-a-part-in-coping-with-social-rejection/] associated with needing more morphine for pain relief after surgery and heightened responses to social rejection. stronger cravings for alcohol; if alcoholic, naltrexone treatment 2x more successful
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
1.6x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). C allele associated significantly (p = 0.021) with post-traumatic stress disorder in a sample of (assumedly Australian) 127 war veterans w/ 228 controls 23andMe blog people with two As at rs6277(T;T) were better at NoGo learning. [pharmgkb] T allele associated with decre...
1.3x increased risk for alcoholism
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rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism. rs1076560 and the DAT 3'-VNTR variant influences memory Genetic variants altering dopamine D2 receptor expression or function modulate the risk of opiate addiction and the dosage requirements of methadone substitution [PharmGKB:Curated This variant is a potential marker for alcoholism. A allele was more prevalent in the alcoholic patients than in the healthy controls in a study consists of 248 alcohol...
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rs806377(C) together with rs6454674(G) make up a haplotype associated (p=0.008) with higher risk of ADHD. In addition, the haplotype was more associated (p=0.03) with ADHD in males than in females with the risk haplotype. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. Evidence for association between polymorphisms in the cannabinoid receptor 1 (CNR1) gene and cannabis dependence. Interaction between two independent CNR1 variants increases risk for cocaine dependence in European Americans: a replication study in family-based sample and population-based sample. Candidate genes for cannabis use disorders: findings, challenges and directions. The association between cannabinoid receptor 1 gene (CNR1) and cannabis dependence symptoms in adolescent...
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This SNP in the GABRA2 gene has been linked to Alcoholism. The effect of this SNP, a synonymous change at amino acid residue 132, is unknown, but it does not change the GABRA2 protein sequence. Carriers of at least one rs279858(G) allele respond slower to the effects of alcohol and are thereby apparently more prone to alcoholism than carriers of two rs279858(A) alleles. Finasteride, an FDA approved drug for the treatment of benign prostatic hypertrophy and a modulator of GABRA2, was shown to have more of a blocking effect on rs279858(A) homozygotes. Note that nearby SNPs have been grouped into a haplotype that shows statistically stronger association with alcohol dependence, namely the haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles . 1050 nicotine-dependent cas...
Frequency: 44.6%
References:1
References:1
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[GWAS:None]
Frequency: 45.1%
References:1
References:1
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[GWAS:None]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
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This snp, located in intron 2 of the central cannabinoid receptor CNR1 gene, has been linked to cannabis dependence. The (G) allele is reported to have a protective effect, and is a defining part of a haplotype that is associated with lower odds of developing cannabis dependence. The (A) allele is more common in all populations studied. Variation in the human cannabinoid receptor CNR1 gene modulates gaze duration for happy faces. (G;G) is also associated with the longest gaze duration for happy faces.
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8;T/T genotypes had significant interaction effects (p = .0003 for comorbid DD and AD, .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806377(C) together with rs6454674(G) make up a haplotype associated (p=0.008) with higher risk of ADHD. In addition, the haplotype was more associated (p=0.03) with ADHD in males than in females with the risk haplotype. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No association of CNR1 gene variations with susceptibility to schi...
Frequency: 54.5%
References:1
References:1
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[GWAS:None]
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8;T/T genotypes had significant interaction effects (p = .0003 for comorbid DD and AD, .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD.
more resistant to treatment for depression
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Based on a study of 256 Caucasian patients being treated for depression, carriers of a rs1049353(G) allele were less likely to respond favorably, particularly if they were females with comorbid anxiety. rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No evidence for an involvement of variants in the cannabinoid receptor gene (CNR1) in obesity in German children and adolescents. The G1422A variant of the cannabinoid receptor gene (CNR1) is associated with abdominal adiposity in obese men. No association of...
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
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[GWAS:None]
lower odds of psychosis
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rs2494732 is a SNP in the AKT1 gene, encoding one of three serine/threonine-protein kinases regulating numerous processes such as cell survival, growth and angiogenesis. Medical conditions that may be linked to the rarer (minor) rs2494732(C) allele include drug response, schizophrenia, and drug-related psychoses, in particuler, cannabis-related psychosis. A case-control study of 489 first-episode psychosis patients concluded that while rs2494732 was not associated with an increased risk of a psychotic disorder, with lifetime cannabis use, or with frequency of use, there was a significant association between psychosis and cannabis use. rs2494732(C;C) individuals with a history of cannabis use had an increased likelihood of a psychotic disorder (odds ratio 2.18, CI: 1.1 - 4.3) when compared ...
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs32440(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, the results we...
Magnitude: 0
Frequency: 81.0%
Repute:Good
References:2
Frequency: 81.0%
Repute:Good
References:2
common in complete genomics
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Association of the cannabinoid receptor gene (CNR1) with ADHD and post-traumatic stress disorder. Cannabinoid receptor 1 (CNR1) gene: impact on antidepressant treatment response and emotion processing in major depression. Cannabinoid receptor 1 gene association with nicotine dependence. Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population. Evidence for association between polymorphisms in the cannabinoid receptor 1 (CNR1) gene and cannabis dependence. Genetic variation in cannabinoid receptor 1 (CNR1) is associated with derangements in lipid homeostasis, independent of body mass index. Candidate genes for cannabis use disorders: findings, challenges and directions. The implication of CNR1 gene's polymorphisms in the modulatio...
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
25 snps
(hide) Cholinesterase Inhibitors
normal
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rs705381, also known as -161C/T and -162A/G, is a SNP in the upstream promoter region of the PON1 gene. (The assumption of equivalence between these names is based on the results of searching for rs705381 in the Variant Name Mapper.) In a study of 101 mostly Caucasian patients prescribed the atypical antipsychotic risperidone, carriers of a rs705381(C) allele were less likely to gain significant weight compared to rs705381(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs8179183 and rs6837793, were also significantly associated with weight profiles in these patients. In a study of 461 participants in the HERITAGE cohort (172 African-American, 289 Caucasian), the combination of rs705381 with 'PON-126' (RS ID unknown) were found to sign...
no positive effect of AChE inhibitors for Alzheimer's patients
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rs733722, also known as -5293C>T, is a SNP near the choline acetyltransferase CHAT gene. A study of 121 Alzheimer's disease patients treated primarily with the acetylcholinesterase (AChE) inhibitors donepezil or galantamine found different rates of mental decline depending on rs733722 genotypes. Individuals of rs733722(C;C) genotype effectively showed declines in cognition over time equivalent to untreated patients, whereas rs733722(C;T) individuals showed less decline, and rs733722(T;T) patients had a negligible decline over the course of the study (~15 months). An earlier study by these authors found no association between SNPs in this gene and actual risk for Alzheimer's.
normal
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
Magnitude: 0
Frequency: 38.9%
References:82
Frequency: 38.9%
References:82
normal
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
0.65x lower risk of ovarian cancer; normal PON catalytic efficiency
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
normal
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
Typical BuChE
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rs1799807, also known as D70G, is a SNP in the BCHE gene. This SNP affects the structure, activity, and substrate specificity of the BuChE (butyrylcholinesterase) enzyme. [Cholinesterases and cholinesterase inhibitors, p. 48] The variant form, rs1799807(G), replaces aspartate with glycine at the secondary substrate/inhibitor binding site. This single base substitution yields the 'atypical' version of BChE. This version has a lower affinity for many substrates, including many Cholinesterase Inhibitors (CIs). A different cholinesterase (acetylcholinesterase, AChE) is an important component of neurotransmission by acetylcholine (ACh), terminating the action of ACh after it has been released during neurotransmission. BChE is found widely in the plasma and normally binds to CIs, protecting AChE...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar common
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(T;T) has a moderate change in BCHE activity according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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(T;T) abolishes catalytic activity in BCHE according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 2]
9 snps
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One copy of H63D, carrier of hemochromatosis, likely unaffected unless also C282Y carrier. You are a carrier for rs1799945(G) H63D Hereditary hemochromatosis. You are unlikely to be affected unless also a carrier of rs1800562(A) C282Y, but others in your family may be. This is a treatable condition.
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rs1799945 represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutations are commonly found in people with Eu...
probably light-skinned, European ancestry This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.
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This SNP influences skin pigmentation. The allele p.A111T, rs1426654(A), indicates light-skinned european ancestry. It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned. This SNP is one of three from the SLC24A5 gene that can be analyzed to categorize the ancestry of a person as either European, African, or Asian, based on a 2009 study. The 3 SNPs are: * rs1426654 * rs2555364 * rs16960620 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER]
more pain [http://blog.23andme.com/2009/08/13/snpwatch-genetic-variation-in-morphine-receptor-may-play-a-part-in-coping-with-social-rejection/] associated with needing more morphine for pain relief after surgery and heightened responses to social rejection. stronger cravings for alcohol; if alcoholic, naltrexone treatment 2x more successful
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
Magnitude: 2.5
Frequency: 38.9%
Repute:Bad
References:104
Frequency: 38.9%
Repute:Bad
References:104
increased risk for type-2 diabetes
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rs13266634 is a SNP in the zinc transporter protein member 8 SLC30A8 gene that has primarily been associated with type-2 diabetes in several studies. This SNP is also known as the Arg325Trp or R325W variant; the (C) allele encodes the arginine (R), and the (T) allele encodes the tryptophan (W). significantly associated p = 0.0073; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls The major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion, but not with insulin resistance. 46% of European non-diabetic offspring of type-2 diabetes patients are rs13266634(C;C) homozygotes; they are diabetes-prone and characterised by a 19% decrease in first-phase insulin release following an intravenous glucose load. * Note: this SNP,...
2.5x risk for AMD; higher mortality among nonagenarians To minimize your risk of age related macular degeneration, consider a diet rich in vitamins C and E, lutein, zeaxanthin and the minerals zinc and copper, such as kale, spinach and broccoli. source
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rs1061170 is a SNP in the complement factor H CFH gene; it is also known as Tyr402His. The rs1061170(T) allele encodes the more common Tyr (Y), while the generally rarer rs1061170(C) encodes the His (H). This SNP has been associated primarily with age related macular degeneration, and to a lesser extent, with longevity. This research paper shows that CFH Y402H is the relevant mutation. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD. rs1061170 (aka Y402H 1277 T>C) was not associated with exudative AMD. CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese CFH variant rs1061170 Y402H is strongly associated with both dry and wet AMD rs1061170(C) alleles are significantly associa...
mix of muscle types this genotype indicate somewhat impaired muscles
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
Accelerated lung decline in smokers
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
3.9x increased risk for cerebral ischemia
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rs4673, also known as C242T or H72Y, is a SNP in the NAD(P)H oxidase p22(phox) subunit CYBA gene. A study of German patients with ischemic stroke or transient ischemic attack under the age of 50 (n = 161) concluded that rs4673(T;T) individuals were almost 4 times more likely to experience cerebral ischemia (odds ratio 3.85, CI: 1.39-10.64) compared to rs4673(C;T) or (C;C) individuals after adjusting for classical risk factors. A meta-analysis concluded that the T allele effect may vary between ethnicities in both direction of effect and significance; Asian populations may have reduced coronary artery disease risk associated with the T allele. Genetic polymorphisms and susceptibility to lung disease. Genetic association of glutathione peroxidase-1 with coronary artery calcification in type ...
~0.80x reduced cancer risk
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rs763110, also known as -844C>T, is a SNP in the FAS ligand FASLG gene. A meta-analysis of 19 published studies, including 11,105 cancer cases and 11,372 controls, concluded that the rs763110(C;T) and (T;T) genotypes were associated with a significantly reduced (about 0.80x) cancer risk of all cancer types.
Magnitude: 2
Frequency: 23.2%
References:10
Frequency: 23.2%
References:10
wet earwax
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rs17822931, also known as c.538G>A or G180R, is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 11 ABCC11 gene. This SNP determines wet vs dry earwax as well as sweat production, it is also associated with lipid secretion. It is commonly (T;T) for asians and (C;C) for europeans and africans. gnxp indicates this SNP influences risk of breast cancer in Japanese women. This does not hold true in Caucasian women, though. reddit discussion [OMIM:ATP-BINDING CASSETTE, SUBFAMILY C, MEMBER 11; ABCC11]
1.6x+ risk of ARMD
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rs2230199, a SNP in the complement component C3 gene, has been reported by several investigators to be associated with ARMD. The common allele at this SNP is known as Arg102; the variant and risk allele is known as Gly102. The risk allele, in orientation to the dbSNP entry for this rs#, is (G). In one of the largest case-control studies, the odds ratio associated with heterozygotes is 1.61, and for homozygotes, 3.26 (p = 4.5 x 10e-12). NEJM reports significant associate with ARMD. blog post [PharmGKB:Curated rs2230199 was found to be associated with risk of age-related macular degeneration in English and Scottish case-control studies.] [OMIM:MACULAR DEGENERATION, AGE-RELATED, 9; ARMD9] [GWAS:Age-related macular degeneration]
1.8x increased risk for high blood pressure
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rs4961 is a variation in the adducin 1 ADD1 gene, encoding a change from a glycine to a tryptophan, so it is also known as G460W or Gly460Trp. Originally, a study of 477 Italian patients indicated that carriers of one or two rs4961(T) alleles were at 1.8x increased risk for hypertension (CI: 1.32-2.43). This study also indicated that carriers of the risk (T) allele responded better to diuretics and sodium-restricted diets, in that they tended to lower their blood pressure by ~10 mmHg points compared to rs4961(G;G) homozygotes similarly treated. Subsequent studies have tended to confirm this association, and to extend it to risk for heart disease. They also have tended to confirm that risk allele carriers respond better to therapy. In a study of ~2200 Belgian patients, rs4961(T) carriers we...
5% higher risk of Age related macular degeneration
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rs800292 is a SNP in the complement factor H CFH gene; it has been linked to blindness in age related macular degeneration. This SNP is also known as 184G>A, I62V, or Val62Ile. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese A study of Chinese AMD patients reports that carriers of both rs11200638 and rs800292 risk alleles pushes the odds ratio for AMD up to 23x. Overall, an 'extremely high' population attributable risk (PAR) of 78% reported for these SNPs. rs800292 was associated with polypoidal choroidal vasculopathy (PCV) in a study of 130 Japanese patients. age related macular degeneration Susceptibility genes for age-re...
Homozygous for CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
possible increased risk for breast cancer
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G), encoding the His; the SNP is also known as N372H or Asn372His. In a separate study, rs144848(G;G) homozygotes were determined to have a 1.31x increased risk (CI: 1.07-1.61) for breast cancer greater risk compared to (T;T) genotypes. Interestingly, in normal females of all ages there is a significant deficiency of homozygotes compared with that expected from Hardy-Weinberg equilibrium, whereas in males there...
carrier Since this comes from omim, it's supposed to be a rare disorder, but HapMap shows that variation is common
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Variation in the ATP-binding cassette transporter 2 gene is a separate risk factor for systemic lupus erythematosus within the MHC. [OMIM:PEPTIDE TRANSPORTER PSF2 POLYMORPHISM]
1.3x increased risk for age-related macular degeneration
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rs1047286 is a SNP in the complement component C3 gene. A 2011 meta-analysis of seven studies concluded that, at least for Caucasians, the rs1047286(C;T) and (T;T) genotypes had 1.27 (CI: 1.15 - 1.41) and 1.70 (CI: 1.27 - 2.11) times higher risk of ARMD than did (G;G) genotypes. [OMIM:C3 POLYMORPHISM, HAV 4-1 PLUS/MINUS TYPE]
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[GWAS:None]
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rs569108, a SNP in the MS4A2 gene, has been linked in a Japanese population to a predisposition to childhood asthma, with an odds ratio of 3 . The risk allele in dbSNP orientation is (C). [Note: no (C;C) homozygotes were observed in this population.] Gene-environment interaction effects on the development of immune responses in the 1st year of life. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients. Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. A candidate gene association...
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
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[OMIM:?]
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Polymorphisms in the NMDA subunit 2B are not associated with alcohol dependence and alcohol withdrawal-induced seizures and delirium tremens. Association analysis of GRIN2B, encoding N-methyl-D-aspartate receptor 2B subunit, and Alzheimer's disease. Association between NMDA receptor subunit 2b gene polymorphism and Alzheimer's disease in Chinese Han population in Shanghai. Variations in the GRIN2B gene are associated with risky decision-making. Variation in the NMDA receptor 2B subunit gene GRIN2B is associated with differential language lateralization.
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[OMIM:?]
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[OMIM:?]
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[GWAS:Platelet counts]
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haplogroups
Frequency: 11.6%
References:2
References:2
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Mutation of ARHGAP9 in patients with coronary spastic angina. [OMIM:?]
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rs1051740, also known as Tyr113His, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. severe hypersensitivity syndrome, triggered by carbamazepine in the presence of a concomitant active human herpes virus (HHV) 6 and 7 infection with the allele HLA-A*3101 and rs1051740(C;C) [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a logistic regression model adjusted for history of phenytoin use during the first trimester and maternal epilepsy, the maternal EPHX1 113 H (rs1051740 T/C) allele was associated with craniofacial abnormalities in the child. Study size: 157 pregnancies. Study population/ethnicity: phenytoin use during the first trimester and maternal epilepsy. metric(s): per rare allele OR: 2.43, 95% confidence interval (CI): 1.16-5.10, P=0.02. Type of asso...
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[OMIM:INSULIN RESISTANCE, SUSCEPTIBILITY TO]
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age related macular degeneration [OMIM:COMPLEMENT FACTOR B; CFB] [GWAS:Age-related macular degeneration]
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[OMIM:?]
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[OMIM:MYOCARDIAL INFARCTION, DECREASED SUSCEPTIBILITY TO]
Frequency: 19.5%
References:1
References:1
Frequency: 19.5%
References:2
References:2
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Endometrial cancer risk is associated with variants of the mismatch repair genes MLH1 and MSH2. Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers. Association between DNA damage response and repair genes and risk of invasive serous ovarian cancer. Recurrent germline mutation in MSH2 arises frequently de novo. MLH1 -93G>A promoter polymorphism and the risk of microsatellite-unstable colorectal cancer. Implications of mismatch repair genes hMLH1 and hMSH2 in patients with sporadic renal cell carcinoma.
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[SNP pentaplex--the allele frequency database of central Poland population]. [The central Poland population database of 500 SNP alleles]. [The usefulness of SNP markers for analyses of highly degraded biological materials]. [OMIM:?]
reported to influence perception of pain
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rs6746030 is a SNP in the sodium channel Nav1.7 SCN9A gene. In five cohorts tested, totaling 1,277 individuals, the rarer rs6746030(A) allele was associated with increased pain (p=0.0001).
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[OMIM:ARYLSULFATASE A POLYMORPHISM]
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[PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): P = 4.7 x 10(-11). Type of association: CO; GN] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:HDL cholesterol]
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. [OMIM:?]
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[GWAS:Lipoprotein-associated phospholipase A2 activity and mass]
Frequency: 28.3%
References:0
References:0
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Sequence variants of the DFNB31 gene among Usher syndrome patients of diverse origin. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Identification of a novel frameshift mutation in the DFNB31/WHRN gene in a Tunisian consanguineous family with hereditary non-syndromic recessive hearing loss.
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finds no association between rs709932 and pulmonary emphysema [OMIM:PI M4]
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[GWAS:Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined)]
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[OMIM:?]
Frequency: 31.0%
References:0
References:0
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18067C>T possibly related to non-Hodgkin lymphoma rs2040639-AG, contribute to oral cancer risk. pseudo-haplotype with AG-CC genotypes in *2.45x risk rs2040639-rs861539 *5.03x risk rs2040639-rs861539-rs2075685 *10.10x risk rs2040639-rs861539-rs2075685-rs1799782 rs4880(C;T) prostate cancer patients being treated by radiation therapy are more likely (8% compared to 0%, p=0.02) to exhibit a significant increase in grade 2 late rectal bleeding after irradiation than (C;C) or (T;T) patients, based on a study of 135 patients. The odds for this are worse if the patient also has the rs861539(C;T) genotype (14% vs 1%, p=0.002). [OMIM:?]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ABCC6 rs2238472 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX] [OMIM:PSEUDOXANTHOMA ELASTICUM]
Frequency: 31.7%
References:4
References:4
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs35264875-T). This variant is associated with Blond vs. brown hair.] [OMIM:TWO-PORE SEGMENT CHANNEL 2; TPCN2] [GWAS:Blond vs. brown hair]
possibly higher glaucoma risk?
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rs3825942, also known as G153D, a SNP causing an amino acid change in the lysyl oxidase 1 LOXL1 gene, has been linked to exfoliation glaucoma (also known as exfoliation syndrome). This form of glaucoma causes up to 10% of the cases of blindness in many countries, including the US. From the abstract of this study: 'Approximately 25% of the general population is homozygous for the highest risk haplotype and their risk of suffering XFG (exfoliation glaucoma) is over 100 times that of those only carrying low-risk haplotypes.' The risk allele for this SNP is rs3825942(C), as oriented with respect to the dbSNP entry, and it confers a estimated relative risk (by itself) of 27 compared to the (T) allele. The odds ratio is 20.10 (CI 10.80-37.41). [Note that the (C) allele is actually quite common i...
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rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele. influences the risk of breast cancer according to the 23andMe blog 23andMe blog rs1800566 increases susceptibility to Lung cancer 0.48 times for heterozygotes (CT) [PharmGKB:Curated Risk or phenotype-associated allele: C/T. Phenotype: There was no association between the NQO1*2 polymorphism and the risk of anthracycline-related CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 1.04; p = 0.97. Type of association: CO; TOX; ADR.] [OMIM:NAD(...
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A study of 414 (ex)-smokers older than 50 years concluded that vitamin D levels were reduced by 25% in rs7041](T;T) homozygotes (p<0.0001), and even after correction for age, gender and smoking history, they were also at increased risk for chronic obstructive pulmonary disease (COPD; odds ratio 2.11, CI: 1.20-3.71, p=0.009). They conclude that since vitamin D deficiency occurs frequently in COPD and correlates with its severity, vitamin D supplementation may be warranted in patients with severe COPD, and especially in those carrying rs7041(T) alleles. [OMIM:?]
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Susceptibility genes for gentamicin-induced vestibular dysfunction.
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[PharmGKB:In-Depth Has been studied in association with long QT.] [OMIM:SODIUM CHANNEL, VOLTAGE-GATED, TYPE V, ALPHA SUBUNIT; SCN5A]
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[OMIM:?]
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rs2227564 A functional polymorphism within plasminogen activator urokinase (PLAU) is associated with Alzheimer's disease . *rs2227564 distribution of four tagSNPs (rs2227562 in intron 5, rs2227564 in exon 6, rs2227571 in intron 9, and rs4065 in 3' UTR) in the PLAU gene in a large case-control study of Alzheimer's disease No association of a non-synonymous PLAU polymorphism with Alzheimer's disease and disease-related traits. Elevated amyloid beta protein (Abeta42) and late onset Alzheimer's disease are associated with single nucleotide polymorphisms in the urokinase-type plasminogen activator gene. Linkage disequilibrium patterns and tagSNP transferability among European populations. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disea...
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Higher lipoprotein-associated phospholipase predicts cardiovascular disease rs2033547 rs1051931 rs10520358 asthma related [OMIM:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
higher risk for COPD
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rs1800469, a SNP in the promoter region of the transforming growth factor beta1 TGFB1 gene has been associated with increased risk for chronic obstructive pulmonary disease (COPD). Although smoking is the main risk factor, smokers with a rs1800469(C) allele (or 2 other TGFB1 SNPs, rs1982073 and rs2241712) were more likely to develop COPD, based on a study of ~700 Caucasian subjects [PharmGKB:Curated T allele associated with increased plasma concentrations of TGFB1;associated with bone density and risk of osteoporosis in postmenopausal Japanese women; may be related to development of asthma;C allele associated with familial vesicoureteral reflux; TT may be associated with increased risk of colorectal adenoma; may be associated with decreased risk of colorectal carcinoma; CC associated with...
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rs20541 influences the effect of maternal smoking during pregnancy and persistent childhood asthma rs1295685 and rs20541 were significantly associated with elevated IgE levels in pooled analyses. rs2569190(T;T) and rs2569191(C;C) genotypes associated with lower IgE 23andMe blog psoriasis Europeans rs20541(G) 1.27x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 5q31.1; Reported Gene(s): IL13; Risk Allele: rs20541-G); (p-value= 0.000000000000005).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEPTIBILITY 11; PSORS11] [GWAS:Psoriasis]
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A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. [OMIM:?]
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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Category:is a snp Homozygosity for the rs2593813]:G-rs4917:Met-rs4918:Ser haplotype conferred an increased risk for leanness [OMIM:ALPHA-2-HS-GLYCOPROTEIN; AHSG]
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[PharmGKB:Curated shortened QT interval]
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Linked to breast cancer [OMIM:LONGEVITY, REDUCED]
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rs4917 is thought to regulate body fat levels and insulin sensitivity. see obesity link1 the MET/MET genotype has been previously linked with reduced plasma lipid levels and lower body fat concentrations. link2 Homozygosity for the rs2593813:G-rs4917:Met-rs4918:Ser haplotype conferred an increased risk for leanness (odds ratio=1.90, P=0.027). [OMIM:ALPHA-2-HS-GLYCOPROTEIN; AHSG]
Frequency: 38.9%
References:1
References:1
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[OMIM:?]
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827 males and 709 females, 606 subjects without cancer and 930 subjects with various cancers *rs1041981(A;C) (C804A, T60N) associated with lung cancer (CA + AA: CC, adjusted OR = 0.60, 95% CI = 0.37 - 0.97), in males but not in females [OMIM:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
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[OMIM:?]
Frequency: 39.8%
References:22
References:22
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rs17266594 rs10516487 rs3733197 gene associated with systemic lupus erythematosus. The association between rs10516487 and lupus was replicated in a study of 1892 European-derived SLE patients and 2652 European-derived controls; the odds ratio observed was 1.22 (CI: 1.11-1.34, corrected p-value=2.59 x 10e-5). [PharmGKB:Curated GWAS Results: Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus (Initial Sample Size: 279 cases, 515 controls; Replication Sample Size: 1,757 cases, 1,540 controls; Risk Allele: rs10516487-G).] [OMIM:B-CELL SCAFFOLD PROTEIN WITH ANKYRIN REPEATS 1; BANK1] [GWAS:Systemic lupus erythematosus]
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
higher risk of LDD
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The rs2073711 SNP (1184T→C ) is located in exon 8 of the cartilage intermediate layer protein gene (CILP). However, CILP gene is primarily known to be expressed abundantly in intervertebral discs, and was reported to have increased expression when degeneration occurs . For the rs2073711 SNP, the ancestral allele is T and the disease associated risk allele is C. A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. ==Background== Low back pain (LBP) is an enervating condition that affects 70-85% of all people during their lifetime . It can lead to decreased physical activity and quality of life, presenting considerable negative socioeconomic and health impacts on m...
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Imputation-based analysis of association studies: candidate regions and quantitative traits. Genetic variants and susceptibility to neurological complications following West Nile virus infection.
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rs6323 (Ile27Leu) is a SNP in located within the HNF1A (Hepatocyte nuclear factor 1 homeobox A) gene. The C allele encodes for the Leu variant. among 356 unrelated Japanese men, lower HDL cholesterol was observed in those with the Ile/Ile genotype (and higher in the Leu/Leu genotype) minor alleles of rs1169288, rs1169286, rs2464196, rs1169310 constitutes a common haplotype (freq. 30%) associated with lower CRP levels [PharmGKB:Curated In a candidate gene-based association analysis of 4333 European-descended, age 65 or older, subjects from the CHS (Cardiovascular Health Study), this was one of the SNPs most strongly associated with plasma C-reactive protein levels. The minor allele is part of a haplotype of frequency 30% which was associated with lower levels of CRP.] [OMIM:INSULIN RESISTA...
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Neural tube defects and folate pathway genes: family-based association tests of gene-gene and gene-environment interactions. Environmental influence on the worldwide prevalence of a 776C->G variant in the transcobalamin gene (TCN2). Folate and one-carbon metabolism gene polymorphisms and their associations with oral facial clefts. Folate-related gene polymorphisms as risk factors for cleft lip and cleft palate. Germline polymorphisms in the one-carbon metabolism pathway and DNA methylation in colorectal cancer. Gene-gene interactions in the folate metabolic pathway and the risk of conotruncal heart defects. Polymorphic variants of genes involved in homocysteine metabolism in celiac disease. Folate and choline metabolism gene variants in relation to ovarian cancer risk in the Polish popu...
Frequency: 43.4%
References:1
References:1
increased risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
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finds no association between rs1303 and pulmonary emphysema [OMIM:PI M3] [GWAS:Metabolite levels]
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[OMIM:?]
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[OMIM:?]
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[OMIM:?]
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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[OMIM:?]
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[OMIM:?] [GWAS:Serum metabolites]
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For this particular SNP, the risk (minor) allele is (G). For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry or BRCA1 and BRCA2.
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, including: * A 1...
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The T allele appears to be protective against high myopia.
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
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rs1076991 C > T exerts a significant effect on promoter activity in vitro and along with rs2236225 G > A influences embryonic development. Common genetic polymorphisms affect the human requirement for the nutrient choline. Neural tube defects and folate pathway genes: family-based association tests of gene-gene and gene-environment interactions. Gene response elements, genetic polymorphisms and epigenetics influence the human dietary requirement for choline. Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not. Folate and one-carbon metabolism gene polymorphisms and their associations with oral facial clefts. Association of polymorphisms in one-carbon metabolizing genes and lung cancer risk: a case-cont...
1.3x increased risk for heart disease
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rs5174 encodes a variant of the LRP8 gene, encoding the low density lipoprotein receptor-related 8 protein (or the apolipoprotein e receptor). The variant affects the protein, changing an arginine to a glutamine; depending on the publication, it can be referred to by terms like R952Q or Arg952Gln. In three Caucasian populations combined, the odds ratio for coronary artery disease or myocardial infarction (and thus heart disease) is 1.31 (adjusted p=0.0003). Note that this association was only seen in populations with familial and premature disease, as a study of 1,231 patients with primarily late-onset, sporadic heart disease did not show any correlation with this SNP. rs5174 (or its equivalent, rs5177) was analyzed in 1,210 patients with familial MI and 1,015 controls from the German MI F...
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[OMIM:OVARIAN RESPONSE TO FSH STIMULATION]
normal risk
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rs6166, also known as Asn680Ser, is a SNP in the follicle stimulating hormone receptor FSHR gene. rs6166(G) is the risk allele encoding the Ser amino acid, at least based on one study in which less fecund women were found to be disproportionately Ser/Ser homozygotes (i.e. rs6166(G;G) homozygotes; p=0.0035). [OMIM:OVARIAN RESPONSE TO FSH STIMULATION]
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mentioned as potentially affecting white matter volume, sample size tiny
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[OMIM:?]
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[OMIM:?]
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[OMIM:?]
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphism in GCKR inversely modula...
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[OMIM:SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE]
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[OMIM:SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE]
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Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.
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798 invasive breast cancer cases and 843 unaffected controls *rs454886 per allele odds ratio, 1.23; 95% confidence intervals, 1.05-1.43; P(trend) = 0.01 [PharmGKB:Curated In 798 invasive breast cancer cases and 843 unaffected controls this SNP in the APC tumor suppressor gene was associated with increased breast cancer risk.] [OMIM:?]
1.5x increased prostate cancer risk
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rs486907 is a SNP in the RNase L RNASEL gene that has been associated with cancer risk. The basic rationale behind most of these studies is that RNase L is responsible for deactivating RNA-based viruses that are associated with certain cancers, and therefore SNPs that lead to lower RNase L activity may lead to increased cancer risk. This SNP is also known as R462Q or Arg462Gln. In a study of prostate cancer patients, rs486907(A;G) heterozygotes were calculated to be at 1.5x increased risk, and rs486907(A;A) homozygotes 2x risk (p=0.007). This SNP was also associated with hereditary-prostate-cancer (HPC) predisposition with an odds ratio of 1.97 (p=0.07) in a study of 116 affected Finnish families. See also: [OMIM:PROSTATE CANCER, SUSCEPTIBILITY TO]
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rs1801280 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801280(C). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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[OMIM:HYPERTRIGLYCERIDEMIA, SUSCEPTIBILITY TO]
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[OMIM:G30 GENE]
2.67x increased risk for systemic sclerosis
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rs2834167 is a SNP in the interleukin-10 receptor 2 IL10RB gene. In a study of Japanese patients, rs2834167(A;A) individuals were at increased risk for diffuse cutaneous systemic sclerosis (odds ratio 2.67, p = 0.0018). [OMIM:?]
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obesity Q223R rs1137101 may be associated with obesity in women with a psychotic disorder treated with atypical antipsychotic drugs Gln223Arg polymorphism could be considered a disease susceptibility modulating factor both in ischemic heart disease or dilated cardiomyopathy patients. [OMIM:LEPTIN RECEPTOR POLYMORPHISM]
None
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Also known as I128T MTP rare allele of the MTP I128T polymorphism may be protective against impaired glucose tolerance, type-2 diabetes Association of polymorphisms in glutamate-cysteine ligase catalytic subunit and microsomal triglyceride transfer protein genes with nonalcoholic fatty liver disease. [OMIM:MICROSOMAL TRIGLYCERIDE TRANSFER PROTEIN, 88-KD; MTP]
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Robust and comprehensive analysis of 20 osteoporosis candidate genes by very high-density single-nucleotide polymorphism screen among 405 white nuclear families identified significant association and gene-gene interaction. SNP combinations in chromosome-wide genes are associated with bone mineral density in Taiwanese women. Genetic variation in candidate osteoporosis genes, bone mineral density, and fracture risk: the study of osteoporotic fractures. [OMIM:?]
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[OMIM:?]
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[OMIM:?] [GWAS:None]
Frequency: 59.5%
References:9
References:9
slightly increased risk for several autoimmune diseases
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rs12150220 is a SNP in the NLRP1 gene, which encodes the NACHT leucine-rich-repeat protein 1. SNPs in this gene may be involved in higher risk for several autoimmune diseases. In a study investigating large patient cohorts from six different autoimmune diseases, including autoimmune Addison's disease (n=333 patients), type-1 diabetes (n=1086), multiple sclerosis (n=502), rheumatoid arthritis (n=945), systemic lupus erythematosus (n=156) and juvenile idiopathic arthritis (n=505), plus 3273 healthy controls, the rs12150220(A) allele was associated with higher risk for both autoimmune Addison's disease (odds ratio 1.25, CI: 1.06-1.49, p = 0.007) and type-1 diabetes (odds ratio 1.15, CI: 1.04-1.27, p = 0.005). [OMIM:NLR FAMILY, PYRIN DOMAIN-CONTAINING 1; NLRP1]
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Epistatic and pleiotropic effects of polymorphisms in the fibrinogen and coagulation factor XIII genes on plasma fibrinogen concentration, fibrin gel structure and risk of myocardial infarction. Sickle cell leg ulcers: associations with haemolysis and SNPs in Klotho, TEK and genes of the TGF-beta/BMP pathway. Comparison of PrASE and Pyrosequencing for SNP Genotyping. The association between fibrinogen haplotypes and myocardial infarction in men is partly mediated through pleiotropic effects on the serum IL-6 concentration. Genetics of atherothrombotic and lacunar stroke. Use of genome-wide expression data to mine the 'Gray Zone' of GWA studies leads to novel candidate obesity genes. Pharmacogenetic aspects in therapeutic management of subfoveal choroidal neovascularisation: role of factor ...
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rs2230806, also known as Arg219Lys or R219K, is a SNP in the ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1 gene. The rs2230806(G) allele encodes the arginine (R), and the (A) allele encodes the lysine (K). A meta-analysis published in 2011 comprising 22 studies with 6597 cases and 15,369 controls studied the association between the rs2230806 and risk for coronary artery disease. Overall, rs2230806(A) significantly associated with a higher HDL-C level in Asians and does lower the risk (odds ratio 0.76, CI: 0.68-0.85, p=3.78e-07) of coronary artery disease in Asians and Caucasians. ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease. Gender-specific association of ATP-binding cassette transporter 1 (ABCA1) polymorphisms with the risk of l...
normal
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omim 131240 In a study of 103 candidate genes for coronary artery disease and associated phenotypes in the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, Pare et al. (2007) found that HDL cholesterol levels were associated with a lysine-to-asparagine substitution at codon 198 (K198N) of the EDN1 gene in a sex-specific manner. The minor allele T (Asn) of the K198N substitution (dbSNP rs5370) was associated with lower HDL cholesterol values. Women showed a strong association between dbSNP rs5370 and HDL cholesterol (P = 1.3 x 10(-5)), whereas in men no such significant association was identified (P = 0.14). 3x increase in the adjusted odds of being hypertensive of rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, 9CI: 1.02 - 8.19). Afte...
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
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Genetic variation and haplotype structures of innate immunity genes in eastern India. Toll-like receptor signaling pathway variants and prostate cancer mortality. Toll-like receptor polymorphisms and susceptibility to urinary tract infections in adult women. [OMIM:LEGIONNAIRE DISEASE, SUSCEPTIBILITY TO]
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[OMIM:PARKINSON DISEASE, SUSCEPTIBILITY TO]
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among high-grade glioma cases rs1805016 (TT versus GT/GG) was significantly protective against mortality over time [hazard ratios (HR), 0.59; 95% confidence intervals (CI), 0.40-0.88]. The IL4R rs1805016 and rs1805015 TT genotypes were both found to be significantly associated with survival beyond 1 year among patients with high-grade glioma (HR, 0.44; 95% CI, 0.27-0.73 and HR, 0.63; 95% CI, 0.44-0.91, respectively) [OMIM:?]
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blog ENPP1 harbors a mutation with a derived state known to protect against obesity and type II diabetes27 that is present in 90% of non-Africans but virtually absent in Africans K121Q (rs1044498) The Q allele of ENPP1 K121Q is associated with hyperglycemia and insulin resistance in whites. increased fasting plasma glucose (FPG), A1C, fasting insulin, and insulin resistance by homeostasis model assessment (HOMA-IR; all P = 0.01-0.006). Association of ENPP1 gene polymorphisms with hand osteoarthritis in a Chuvasha population. Studies of the relationship between the ENPP1 K121Q polymorphism and type 2 diabetes, insulin resistance and obesity in 7,333 Danish white subjects. Common variants in the ENPP1 gene are not reproducibly associated with diabetes or obesity. ENPP1 K121Q polymorphism and...
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NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP PTPRJ haplotypes and colorectal cancer risk. [OMIM:COLON CANCER, SOMATIC]
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[OMIM:?]
Frequency: 88.5%
References:1
References:1
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[OMIM:?]
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[OMIM:GAMMA-AMINOBUTYRIC ACID RECEPTOR, BETA-3; GABRB3]
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rs1006615 is associated with increased risk for schizophrenia in German and Scandinavian samples
possibly higher glaucoma risk? glaucoma risk likely to actually be based on nearby rs3825942
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rs1048661, also known as R141L, a SNP causing an amino acid change in the lysyl oxidase 1 LOXL1 gene, has been linked to exfoliation glaucoma. This form of glaucoma causes up to 10% of the cases of blindness in many countries, including the US. [Science DOI: 10.1126/science.1146554] From the abstract of this study: 'Approximately 25% of the general population is homozygous for the highest risk haplotype and their risk of suffering XFG (exfoliation glaucoma) is over 100 times that of those only carrying low-risk haplotypes.' The risk allele for this SNP is rs1048661(G), and it confers a estimated relative risk (by itself) of 3.04. The odds ratio is 2.46 (CI 1.91-3.16). [Note that the (G) allele is actually quite common in most European populations.] However, a meta-analysis published in 201...
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[GWAS:None]
References:1
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[OMIM:?]
References:1
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[OMIM:?]
References:1
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[OMIM:?]
References:0
References:1
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[OMIM:?]
References:1
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[OMIM:?]
References:0
References:1
References:1
References:1
References:0
References:1
References:1
References:1
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[OMIM:?]
brown/black eyes more likely
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
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[OMIM:LEGIONNAIRE DISEASE, SUSCEPTIBILITY TO]
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asthma related influences sleep patterns [http://originsgenomeresources.net/musings/?p=62] [OMIM:ASTHMA SUSCEPTIBILITY 2]
normal
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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[OMIM:?]
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[OMIM:?]
no credible risk
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suggested the contribution of rs237025 to type-1 diabetes, however in this failed to replicate. This SNP is also known as Met55Val, M55V, or A163G. This was the first SNP in SNPedia. The type 1 diabetes susceptibility gene SUMO4 at IDDM5 is not associated with susceptibility to rheumatoid arthritis or juvenile idiopathic arthritis. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Evidence for the role of small ubiquitin-like modifier 4 as a general autoimmunity locus in the Japanese population. SUMO4 M55V variant is associated with diabetic nephropathy in type 2 diabetes. Association study of NFKB1 and SUMO4 polymorphisms in Chinese patients with pso...
susceptible to Norovirus infections
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rs601338 is found on chromosome 19 in the alpha(1,2)-fucosyltransferase FUT2 gene. The wild-type rs601338(G) encodes the 'secretor' (Se) allele, while rs601338(A) encodes the 'non-secretor' (se) allele. A study of 115 Swedish adults concluded that rs601338(A;A) homozygotes have genetic immunity to infection by the Norwalk norovirus, a major (and contagious) cause of acute gastroenteritis worldwide among adults. This illness is also known as 'cruise ship gastroenteritis.' Being a non-secretor may have other consequences, such as greater susceptibility to infection by influenza viruses and by some types of bacteria. 23andMe discusses these topics. In some non-Caucasian populations, a different SNP is responsible for non-secretor phenotypes. For example, although the Se allele is absent in Ja...
can taste bitter
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rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you. (G;G)...
Magnitude: 0.1
Frequency: 47.8%
References:6
Frequency: 47.8%
References:6
can taste bitter
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rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
can taste bitter
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*3, defined as the common loss of function variant rs1057910(C) (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/. Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of nonsteroidal anti-inflammatory drugs (NSAIDs) that are CYP2C8 or CYP2C9 substrates, such as aceclofena...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
Magnitude: 0.1
Frequency: 91.8%
Repute:Bad
References:88
Frequency: 91.8%
Repute:Bad
References:88
normal, but higher risk for certain autoimmune diseases
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
common one paper reports increased risk of alcoholism for African-Americans with this genotype.
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This paper found significant association with rs2066702, the SNP that defines ADH1B*3, in African American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B*1, and the low-risk allele encodes ADH1B*3. A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.In some African American] and Native American populations, the ADH1B*3 allele (Arg369Cys in exon 9) is correlated with protection against alcoholism. [PharmGKB:In-Depth This allele has been found in some African American and Native American populations to be correlated with prote...
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-1 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs364897, also known as Asn188Ser or N188S, is a variant in the GBA gene. rs354897(A) encodes the more common Asn at this position. rs364897(G;G) has been observed in Korean and Taiwanese subjects with type I Gaucher disease. It may be a relatively mild defect in the gene, since it appears the encoded enzyme appears to retain most of its function. [OMIM:?]
normal
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rs2241880, a SNP in the ATG16L1 gene encoding a threonine to alanine substitution ('T300A') in a protein known to be involved in the function of the epithelial cells lining the intestine, has been associated with Crohn's disease in several recent studies. In another recent (2007) report, rs2241880 is confirmed to be associated with both Crohn's disease and ileal disease, but additionally, the authors calculate risk for individuals who are homozygotes for this SNP plus 2 others (in the IBD5 and NOD2 genes). Individuals homozygous for the risk alleles for all 3 of these SNPs are estimated to be at 20 fold higher risk (CI ~9-49) for Crohn's disease. From the largest most recent survey, the Crohn's disease-associated SNPs for IBD5 and NOD2 are, respectively, rs6596075 and rs17221417. associate...
normal
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rs2303067, a SNP in the SPINK5 gene, has been significantly associated with susceptibility to atopic dermatitis. The risk allele for rs2303067 is (A). rs2303067 has also been associated with predisposition to asthma, . From this study: 'A significant association between rs2303067 and the development of asthma was observed (OR 1.77; 95%CI: 1.02-3.06, P=0.041 for rs2303067(A;A) homozygotes). Atopic carriers of rs2303067 showed an increased risk for asthma and asthma symptoms (OR 2.06; 95%CI: 1.01-4.20, P=0.047). When children with a combination of asthma and atopic dermatitis were compared with normal controls, the rs2303067(A) genotype was more prevalent in the disease group (OR 4.56; 95%CI: 1.370-15.12, P=0.007).' [OMIM:?]
normal
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and R131H. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
normal
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
normal
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rs213950, a SNP in the cystic fibrosis CFTR gene, has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.09 (CI 1.04–1.15). [OMIM:CFTR POLYMORPHISM]
common in clinvar
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Influences appearance gnxp [OMIM:TWO-PORE SEGMENT CHANNEL 2; TPCN2]
common in clinvar
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rs3762271 is an A/C SNP located in the ASPM gene. The A-allele of this SNP as well as the G-allele of rs964201 another SNP located in the ASPM gene and rs2442496 a SNP in the MCPH1 gene arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans. A comment is provided by g2b2mh.
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
normal
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23andMe blog rs2736098 and rs401681 linked to many cancers [OMIM:BASAL CELL CARCINOMA, MULTIPLE]
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
common
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Rs4504469, a nonsynonymous SNP in exon 4 of the KIAA0319 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (T). The odds ratio in a study of case:control study of ~400 Caucasians associated with rs4504469(T) is 1.51 (CI: 1.17–1.95, p = 0.002). A 77-kilobase region of chromosome 6p22.2 is associated with dyslexia in families from the United Kingdom and from the United States. Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia. A common variant associated with dyslexia reduces expression of the KIAA0319 gene. Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impairment. [OMIM:KIA...
Magnitude: 0
Frequency: 38.9%
References:82
Frequency: 38.9%
References:82
normal
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
Magnitude: 0
Frequency: 39.3%
Repute:Good
References:0
Frequency: 39.3%
Repute:Good
References:0
normal
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Sequence variants of elaC homolog 2 (Escherichia coli) (ELAC2) gene and susceptibility to prostate cancer in the Health Professionals Follow-Up Study. Development of a fingerprinting panel using medically relevant polymorphisms. Genetic variants and prostate cancer risk: candidate replication and exploration of viral restriction genes. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project. [OMIM:PROSTATE CANCER, SUSCEPTIBILITY TO]
normal
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rs6280, also known as '''Ser9Gly''', is a SNP in the dopamine receptor D3 DRD3 gene. The rs6280(C) allele encodes a glycine, and the (T) allele encodes a serine (in dbSNP orientation). In a study of 88 patients being treated for schizophrenia with olanzapine, those who were rs6280(C;C) homozygotes had greater positive symptom remission (endpoint rating of minimal or none on all PANSS clinical response positive items, 39.1%), as compared with (C;T) or (T;T) genotypes (13.8%; p = 0.033). Ser9Gly has been implicated in executive function in some studies, but the results are conflicting. * Gly/Gly carriers showed significantly (p = 0.002) poorer performance than Ser/Ser carriers on executive functioning tasks in a somewhat small Caucasian sample (84 patients with first-episode psychosis and 85...
common in clinvar
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Nicotine dependence in a prospective population-based study of adolescents: the protective role of a functional tyrosine hydroxylase polymorphism. Discovery of common human genetic variants of GTP cyclohydrolase 1 (GCH1) governing nitric oxide, autonomic activity, and cardiovascular risk. Dopa decarboxylase and tyrosine hydroxylase gene variants in suicidal behavior. A functional intronic variant in the tyrosine hydroxylase (TH) gene confers risk of essential hypertension in the Northern Chinese Han population. Financial and psychological risk attitudes associated with two single nucleotide polymorphisms in the nicotine receptor (CHRNA4) gene. Overview of the Rapid Response data. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. ...
common in clinvar
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Development of a fingerprinting panel using medically relevant polymorphisms. Genetic risk factors for hepatopulmonary syndrome in patients with advanced liver disease. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. von Willebrand factor plasma levels, genetic variations and coronary heart disease in an older population. [GWAS:Coagulation factor levels]
common in clinvar
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rs3738401 is a SNP in the DISC1 gene, known as R264Q. Associated with schizophrenia 13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. *under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059). [OMIM:DISRUPTED IN SCHIZOPHRENIA 1; DISC1]
normal
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rs351855, a SNP in the fibroblast growth factor receptor 4 (FGFR4) gene, is also known as the Gly388Arg variant. The rs351855(T) allele encodes the risk (Arg) allele. The Arg form of this SNP is likely to cause a harder to treat version of node-positive breast cancer, including reducing the efficacy of Herceptin, based on a study of 372 patients. A study of ~500 Japanese prostate cancer patients found that individuals with a rs351855(T;T) genotype had a 2.2- and 1.9-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 1.8-fold increased risk of metastatic prostate cancer compared to the (C;C) genotype. A meta-analysis published in 2011, surveying a total of 2,618 cases of prostate cancer, concluded that the odds ratio per rs351855(T) allele was 1.17 (CI: 1.07...
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
0.65x lower risk of ovarian cancer; normal PON catalytic efficiency
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
normal
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Testicular cancer patients may be treated with bleomycin, a cytotoxic drug that is essential component of chemotherapy regimens for this cancer, officially known as disseminated testicular germ-cell cancer (TC). rs1050565 is a SNP in the BLMH gene. This gene encodes a protein that can inactivate bleomycin. Based on a study of 300 TC patients treated with bleomycin, a testicular cancer patient with a rs1050565(G;G) genotype has an odds ratio of 4.97 (CI: 2.17 - 11.39) for TC-related death compared to (A;G) or (A;A) genotypes. The rs1050565(G;G) genotype also shows a higher prevalence of early relapses. [PharmGKB:Curated Testicular germ cell cancer patients carrying the homozygous G/G allele of this variant showed reduced survival and higher prevalence of early relapses after treatment with...
better long-term memory?
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rs1799990, also known as Met129Val or M129V, is a SNP in the prion protein PRNP gene. The more common rs1799990(A) allele encodes the Met (methionine). Historically, since 1991 this SNP has been associated with risk for sporadic Creutzfeldt-Jakob disease, with homozygotes of both types apparently at increased risk compared to heterozygotes. More recently, this SNP has been related to long-term memory with (A;A) and (A;G) individuals recalling 17% more words than (G;G) individuals at 24h following learning. A further study of 12 individuals of each of the 3 possible genotypes showed that at both 30 minutes and 24 hour time lags, correlations between retrieval-related brain activity and retrieval success were negative for (G;) homozygotes (the more activity, the worse retrieval success), whi...
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This SNP has been related to exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: CETP V405 valine homozygosity (GG genotype) is asso...
normal
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rs669 is a SNP in the alpha-2-macroglobulin A2M gene. In dbSNP orientation, the rs669(A) allele encodes an isoleucine, and the rs669(G) allele encodes a valine; the SNP is also known as the Ile/Val variant. On its own, rs669 was not seen to reproducibly and independently increase risk for Alzheimer's disease in several studies of ~200 Italian patients. However, the T-C-A haplotype of rs12316150-rs1050283-rs669 was associated with both early- and late-onset Alzheimer's disease. The majority of the disease risk from this haplotype was based on rs1050283. The original 2004 study of 148 Italian sporadic AD patients yielded an odds ratio for the rs669(G;G) genotype (as oriented in dbSNP orientation) of 3.81 (CI: 1.66-8.75). The presence of rs2333227(C;C), in addition to rs669(G;G), appears to s...
common in clinvar
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer * cleft lip and cleft palate * coronary artery disease * depression * hyperhomocysteinemia * migraine * neural tube defects * pre-eclampsia (ges...
common in clinvar
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rs1137100 is a nonsynonymous coding SNP in exon 4 of the leptin receptor LEPR gene. It has been reported to affect glucose tolerance and insulin response, and it is also one of five SNPs reported to be useful in a SNP set defining the risk of dying from prostate cancer among patients with the disease; see gs242 and gs243. [OMIM:LEPTIN RECEPTOR POLYMORPHISM]
common in clinvar
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see rs2282679, a near-perfect proxy for rs4588 Gene-environment interaction effects on the development of immune responses in the 1st year of life. The genetics of chronic obstructive pulmonary disease. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. The Gc2 allele of the vitamin D binding protein is associated with a decreased postmenopausal breast cancer risk, independent of the vitamin D status. Genetic and environmental determinants of 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D levels in Hispanic and African Americans. Genetic polymorphisms of the vitamin D binding protein and plasma concentrations of 25-hydroxyvitamin D in premenopausal women. A meta-analysis of candidate gene polymorphisms and ischemic stroke in ...
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
common in clinvar
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[PharmGKB:Curated Homozygotes for this variant allele in the CTH gene had significantly higher plasma homocysteine levels than other genotypes in a cohort of 496 Caucasian individuals.] [OMIM:?]
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see also rs3732378 [OMIM:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RAPID PROGRESSION TO AIDS]
Magnitude: 0
Frequency: 55.4%
Repute:Good
References:2
Frequency: 55.4%
Repute:Good
References:2
common
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While the ApoE4 allele (rs429358(C)) is widely accepted as the predominant genetic risk factor for Alzheimer's disease, there are likely to be numerous other factors, both genetic and environmental, associated to lesser degrees with susceptibility to the disease. Genes influencing the immune system, and in particular susceptibility to viral infections such as herpes, may be among such factors. This SNP, located in the TAP2 gene and thus implicated in the activation of HIV and HSV-1 viruses, is seen more commonly in ~300 Alzheimer patients than in the same number of controls. The risk allele is rs241448(C). The odds ratio is reported to be 2.14 (CI: 1.02-2.55) for rsrs241448(C;C) homozygotes, and 1.51 (CI: 0.80-1.93) for rsrs241448(C;T) heterozygotes, compared with rsrs241448(T;T) homozygot...
normal
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rs1800255 is a SNP in the alpha I chain of the type III collagen protein-encoding COL3A1 gene. A relatively small study (200 patients) reported an odds ratio of 5 (CI: 1.4-17.1) between rs1800255(A;A) homozygotes and risk for pelvic organ prolapse. [OMIM:?]
common in clinvar
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Haplotypes and gene expression implicate the MAPT region for Parkinson disease: the GenePD Study. The distribution and most recent common ancestor of the 17q21 inversion in humans. Independent and joint effects of the MAPT and SNCA genes in Parkinson disease.
Magnitude: 0
Frequency: 60.0%
Repute:Good
References:2
Frequency: 60.0%
Repute:Good
References:2
Magnitude: 0
Frequency: 61.1%
Repute:Good
References:44
Frequency: 61.1%
Repute:Good
References:44
normal
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rs10490924 was identified as a risk factor from chromosome 10 related to age related macular degeneration. The risk allele is (T). Odds ratios for heterozygotes and homozygotes are, respectively, 2.69 (CI: 2.22-3.27) and 8.21 (CI: 5.79-11.65). Disease risk in combination with the rs1061170 SNP in the CFH gene is dramatically increased. Homozygotes for both the rare/risk alleles at both loci are estimated to be at 57 fold higher risk for age related macular degeneration than individuals homozygous for the common alleles at both loci. A subsequent study indicated that the risk based on solely the ARMS2 SNP rs10490924 is significantly higher in smokers than in non-smokers. Based on a study of ~750 patients, rs10490924 is significantly higher in participants with choroidal neovascularization t...
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[OMIM:URIC ACID NEPHROLITHIASIS, SUSCEPTIBILITY TO] [GWAS:None]
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs32440(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, the results we...
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[OMIM:ATOPY, SUSCEPTIBILITY TO] [GWAS:None]
common in clinvar
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rs2234922, also known as His139Arg, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. The genetics of chronic obstructive pulmonary disease. Orofacial cleft risk is increased with maternal smoking and specific detoxification-gene variants. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Xenobiotic metabolizing enzyme gene polymorphisms predict response to lung volume reduction surgery. Genetic polymorphisms and benzene metabolism in humans exposed to a wide range of air concentrations. Correlating observed odds ratios from lung cancer case-control studies to SNP functional scores predicted by bioinformatic tools. Do genetic factors protect for early onset lung...
normal
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
common on affy axiom data
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[OMIM:CYTOCHROME P450, SUBFAMILY I, POLYPEPTIDE 1; CYP1B1]
A2/A2 bupropion effective
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain , and has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessation success, or finding no such association. A meta-analys...
common in clinvar
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[PharmGKB:Curated This variant may be associated with risk of developing glioma.] [OMIM:MULTIPLE MYELOMA, RESISTANCE TO]
common in clinvar
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Mentioned in a 23andMe discussion on intelligence. Synonymous Polymorphisms at Splicing Regulatory Sites are Associated with CpGs in Neurodegenerative Disease-Related Genes.
common in complete genomics
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Novel sequence variants in the TMC1 gene in Pakistani families with autosomal recessive hearing impairment.
Magnitude: 0
Frequency: 67.7%
Repute:Good
References:1
Frequency: 67.7%
Repute:Good
References:1
common on affy axiom data
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23andMe blog rs8177374(T) less susceptible to infection with malaria, tuberculosis, bacteremia and pneumococcal disease. [PharmGKB:Curated In a case-control study of 6,106 individuals from the UK, Vietnam and several African countries with invasive pneumococcal disease, bacteremia, malaria and tuberculosis the heterozygous carriage of this variant was associated independently with all four infectious diseases in the different study populations. Further this study found a protective effect of S180L heterozygosity against these infectious diseases. A second study could not confirm this association.] [OMIM:TIR DOMAIN-CONTAINING ADAPTOR PROTEIN; TIRAP]
common on affy axiom data
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rs3732378 VAL249ILE is tightly linked to neighboring rs3732379 THR280MET The protein receptor with both variant amino acids is known as CX3CR1-M280. the minor alleles of this pair are associated with *more rapid progression to full-blown AIDS and probably increased susceptibility to HIV infection *reduced risk of acute coronary events *increased risk of age related macular degeneration [OMIM:?]
common in clinvar
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Lysyl oxidase G473A polymorphism is closely associated with susceptibility to gastric cancer in a South Korean population. [OMIM:LYSYL OXIDASE POLYMORPHISM]
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associated with genetic susceptibility to tuberculosis in West Africa Variants in the SP110 gene are associated with genetic susceptibility to tuberculosis in West Africa. Polymorphisms in IL-1beta, vitamin D receptor Fok1, and Toll-like receptor 2 are associated with extrapulmonary tuberculosis. SP110 gene polymorphisms and tuberculosis susceptibility: A systematic review and meta-analysis based on 10 624 subjects. [OMIM:NUCLEAR BODY PROTEIN SP110; SP110]
common in clinvar
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pulmonary morbidity in preterm infants. related to non-Hodgkin's lymphoma Genetic studies of a cluster of acute lymphoblastic leukemia cases in Churchill County, Nevada. Regional association-based fine-mapping for sodium-lithium countertransport on chromosome 10. Pharmacogenetics of minimal residual disease response in children with B-precursor acute lymphoblastic leukemia: a report from the Children's Oncology Group. Genetic variation and haplotype structures of innate immunity genes in eastern India. MBL2 and hepatitis C virus infection among injection drug users. Prevalence in the United States of selected candidate gene variants: Third National Health and Nutrition Examination Survey, 1991-1994. Elevated MBL concentrations are not an indication of association between the MBL2 gene and ...
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
Magnitude: 0
Frequency: 74.1%
Repute:Good
References:1
Frequency: 74.1%
Repute:Good
References:1
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
average
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin use. A protective effect of rs5918 has also been observed for the development of Non-Hodgkin Lymphoma, both...
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:7
Frequency: 76.1%
Repute:Good
References:7
normal
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This position is odd. Under the older build36, it was on the plus strand, as of build37 it is now on the minus strand. This makes is very prone to some ambiguous flip confusion in ther literature, plus 23andMe users self reporting the flipped form. Instead of the usual bi-allelic SNP, all 4 alleles are reported in dbSNP, however this is probably due to the strand changes. dbSNP currently says the normal is C, and T is the rare geno which causes a premature stop, early in the gene. We at SNPedia suspect that the A & G alleles are not common enough to have ever been genuinely reported, but for de-novo mutations each allele would be non-synonymous and result in a different amino acid. http://snpedia.blogspot.com/2012/12/snpedias-nightmare-before-christmas.html rs17602729, a SNP located in the...
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
common in complete genomics
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Meta-analysis of 14 studies did not support a significant association between rs288326 and osteoarthritis. Functional variants within the secreted frizzled-related protein 3 gene are associated with hip osteoarthritis in females. Further evidence of the role of frizzled-related protein gene polymorphisms in osteoarthritis. Power of multifactor dimensionality reduction and penalized logistic regression for detecting gene-gene interaction in a case-control study. No association of the polymorphisms of the frizzled-related protein gene with peak bone mineral density in Chinese nuclear families. Variant alleles of the Wnt antagonist FRZB are determinants of hip shape and modify the relationship between hip shape and osteoarthritis. [OMIM:OSTEOARTHRITIS OF HIP, FEMALE-SPECIFIC, SUSCEPTIBILITY ...
normal
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
common in complete genomics
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rs2066844 is a SNP in the NOD2 gene; the SNP is also known as R702W, with the (C) allele encoding the Arg (R) and the (T) allele encoding the Trp (W). rs2066844 is mentioned in as being strongly associated with Crohn's disease No association was found for NOD2/CARD15 SNPs (R702W, G908R) in Chinese patients with inflammatory bowel disease. [OMIM:CROHN DISEASE, SUSCEPTIBILITY TO]
common in clinvar
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Variations in the peroxisome proliferator-activated receptor-gamma gene and melanoma risk. PPAR-gamma gene polymorphisms and psoriatic arthritis. The Genetics of PPARG and the Skeleton. The association of Pro12Ala polymorphism of peroxisome proliferator-activated receptor-gamma gene with serum osteoprotegerin levels in healthy Korean women. Association of stearoyl-CoA desaturase 1 activity with familial combined hyperlipidemia. Polymorphism of genes related to insulin sensitivity and the risk of biliary tract cancer and biliary stone: a population-based case-control study in Shanghai, China. PPAR Genomics and Pharmacogenomics: Implications for Cardiovascular Disease. Association of FTO with obesity-related traits in the Cebu Longitudinal Health and Nutrition Survey (CLHNS) Cohort. Differen...
common in clinvar
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Compared with individuals without CCR5-Delta32 (a variation in another gene) or rs1799864(A), individuals with one or two copies of rs1799864(A) had a 58% lower risk of developing AIDS during the first 4 years after testing positive for HIV, a 19% lower risk during the subsequent 4 years, and no significant protection thereafter. No protective effect (ie no benefit) was seen for this SNP once AIDS had developed. rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [OMIM:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RESISTANCE TO]
Magnitude: 0
Frequency: 80.5%
Repute:Good
References:8
Frequency: 80.5%
Repute:Good
References:8
common in clinvar
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among 120 (likely Japanese) first-episode neuroleptic-naive schizophrenics treated with risperidone genotyped for 30 variants in misc. dopamine and serotonin (receptors and otherwise) two SNPs in DRD2 (rs1799989 and rs1800497) and two SNPs in AKT1 (rs3803300 and rs2494732) were significant predictors of treatment response to risperidone
Magnitude: 0
Frequency: 81.4%
Repute:Good
References:2
Frequency: 81.4%
Repute:Good
References:2
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Two SNPedia users have self reported the (T;T) genotype with no apparent consequences. It was first noted in a patient with documented in omim. A Japanese patient with the intermediate form of maple syrup urine disease 2 showed a compound heterozygote for both * the apparently causative C->G transversion at nucleotide 309 DBT gene (I37M) * this G->A transition in exon 9 (G323S) which with no obvious consequences [OMIM:?]
common in clinvar
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Transthyretin: no association between serum levels or gene variants and schizophrenia. Association of TTR polymorphisms with hippocampal atrophy in Alzheimer disease families. [OMIM:TRANSTHYRETIN SER-6 POLYMORPHISM]
Magnitude: 0
Frequency: 82.0%
Repute:Good
References:2
Frequency: 82.0%
Repute:Good
References:2
common in complete genomics
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (A).
common in complete genomics
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asthma related [OMIM:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
common in clinvar
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rs1127354 (Pro32Thr/P32T, 94C>A) is a SNP within the ITPA (Inosine triphosphate pyrophosphatase) gene. (note: rs1127354 supersedes rs41320251) abolishes IPTA activity in homozygous individuals and reduces the activity to 25% in heterozygous subjects, mercaptopurine metabolism (sig. higher methyl mercaptopurine nucleotides levels + higher probability of severe febrile neutropenia in A carriers treated with mercaptopurine) Mutations in the gene encoding the Wnt-signaling component R-spondin 4 (RSPO4) cause autosomal recessive anonychia. Pharmacogenomic studies of the anticancer and immunosuppressive thiopurines mercaptopurine and azathioprine. Investigation of candidate polymorphisms and disease activity in rheumatoid arthritis patients on methotrexate. Variants in the ITPA gene protect a...
common in clinvar
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rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair color in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also OMIM 155555.0006 [OMIM:?]
Magnitude: 0
Frequency: 84.1%
Repute:Good
References:1
Frequency: 84.1%
Repute:Good
References:1
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:2
Frequency: 85.0%
Repute:Good
References:2
common on affy axiom data
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23andMe blog rs11170164 T 1.35 Basal Cell Carcinoma [OMIM:?]
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In a study of early onset coronary artery disease, rs9289231, the risk allele of this SNP, located in the kalirin KALRN gene, was associated with increased odds (OR 2.1), and also for increased atherosclerosis burden. [OMIM:KALIRIN; KALRN]
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
common on affy axiom data
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[OMIM:TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL, SUBFAMILY M, MEMBER 7;]
common in clinvar common for Caucasians on the 23andme platform
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rs2228479, known as Val92Met or V92M, is one of several SNPs in the MC1R gene commonly associated with red (or blond) hair and poor tanning, but note its high presence in one Asian population The risk allele is rs2228479(A), compared with the wild-type rs2228479(G) allele. See also OMIM 155555.0002 [OMIM:?]
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also referred to as 1766A/G plos rs450046 was most strongly positively associated with schizophrenia in families. rs372055(C), rs450046(G), rs385440(A) haplotype carriers (n = 32) exhibited attenuated PPI + verbal memory (p < .001) as well as higher anxiety (p < .004) and schizotypy (p < .008) compared to noncarriers (n = 185) Genome bioinformatic analysis of nonsynonymous SNPs. Structural cerebral variations as useful endophenotypes in schizophrenia: do they help construct 'extended endophenotypes'? Functional polymorphisms in PRODH are associated with risk and protection for schizophrenia and fronto-striatal structure and function. Executive function, neural circuitry, and genetic mechanisms in schizophrenia. [OMIM:HYPERPROLINEMIA, TYPE I]
common in clinvar
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Medical sequencing at the extremes of human body mass. Genetic variation in human NPY expression affects stress response and emotion. Neuropeptide Y receptor genes are associated with alcohol dependence, alcohol withdrawal phenotypes, and cocaine dependence. Neuropeptide Y gene polymorphisms confer risk of early-onset atherosclerosis. NPAS2 and PER2 are linked to risk factors of the metabolic syndrome. A systematic meta-analysis of genetic association studies for diabetic retinopathy. CLOCK is suggested to associate with comorbid alcohol use and depressive disorders. Poor replication of candidate genes for major depressive disorder using genome-wide association data. [PharmGKB:Curated This non-synonymous variant in the NYP gene was associate with several conditions and diseases in several...
Magnitude: 0
Frequency: 88.2%
Repute:Good
References:0
Frequency: 88.2%
Repute:Good
References:0
common in complete genomics
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.0000123; OR for minor allele T:0.659)]
normal
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The INSR A-603G promoter rs1864010 SNP, which is located within a known Sp1-binding site, was associated with the risk of colorectal cancer, with carriers of the G allele having a decreased risk (odds ratios (OR) 0.71, 95% confidence interval (CI) 0.54-0.93). Carrying the variant allele of the IRS1 Gly972Arg rs1801278 SNP further decreased the risk among the INSR-603G allele carriers (OR 0.28, 95% CI 0.11-0.70) multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0)
Magnitude: 0
Frequency: 89.3%
Repute:Good
References:2
Frequency: 89.3%
Repute:Good
References:2
common in clinvar
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Functional genetic polymorphisms and female reproductive disorders: part II--endometriosis. 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS). [OMIM:?]
common in clinvar
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DNA-based methods in the immunohematology reference laboratory. [OMIM:?]
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who actually develop...
normal
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rs4986852 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 1040. The more common rs4986852(G) allele encodes Ser, while the rare rs4986852(A) allele encodes Asn; this variation is also known as Ser1040Asn or S1040N. A well known study published in 1994 looked at 10 family pedigrees with breast cancer and ovarian cancer susceptibility, including 63 breast cancer patients, and discovered what they believed were seven putative disease-causing mutations. rs4986852 was one of these variants. * See also Omim 113705.0011 [OMIM:?]
common in complete genomics
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*rs6232 G allele (in dbSNP orientation) linked to 1.34x increased risk of obesity *rs6234/rs6235 (or rs10515237) see also: spitoon Obesity: Preliminary Research [PharmGKB:Curated In a study at 13,659 individuals of European ancestry the N221D variant was consistently associated with obesity in adults and children.] [OMIM:PROPROTEIN CONVERTASE, SUBTILISIN/KEXIN-TYPE, 1; PCSK1]
Magnitude: 0
Frequency: 91.5%
Repute:Good
References:0
Frequency: 91.5%
Repute:Good
References:0
normal risk
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rs1801270 is a SNP known as p21 codon 31, although the gene now known to code for the p21 protein is termed CDKN1A, and has also been known as WAF1 and CIP1. Along with p53 codon 72 (rs1042522), it is one of the best studied SNPs due to its role in increased tumor susceptibility (and thus cancer). A study of ~150 lung cancer patients in Sweden found that the rs1801279(A) allele, encoding the amino acid Arg at codon 31, represented the risk allele (odds ratio 1.7, CI: 1.0-2.9), compared to healthy individuals. The difference was even more striking when compared to patients with chronic obstructive pulmonary disease (COPD), in which case the odds ratio was over 5. [OMIM:CIP1/WAF1 TUMOR-ASSOCIATED POLYMORPHISM 1]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:4
Frequency: 92.0%
Repute:Good
References:4
common in clinvar
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Previous studies had suggested that the minor allele of this SNP might influence breast cancer. However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. [OMIM:?]
normal breast cancer risk
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. This particular SNP, rs1799950, was actually the only SNP of the 25 to have an increased odds ratio for breast cancer to be over 1.5 in carriers and to also be present at a minor allele frequency of over 5%. The odds ratio calculated was 1.72 (P = 0.0002). The risk (minor) allele is (G).
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:3
Frequency: 92.9%
Repute:Good
References:3
common in complete genomics
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The A allele of rs1799899, also known as the human transferrin G277S mutation, is associated with iron deficiency anemia , lower total iron binding capacity (TIBC), and anemia in menstruating white women. [OMIM:IRON DEFICIENCY ANEMIA, SUSCEPTIBILITY TO] [GWAS:None]
common on affy axiom data
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[PharmGKB:Curated May be associated with clefts of the lip, alveolus, and palate.]
common in clinvar
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Interferon regulatory factor 6 (IRF6) and fibroblast growth factor receptor 1 (FGFR1) contribute to human tooth agenesis. Association between IRF6 and nonsyndromic cleft lip with or without cleft palate in four populations. Genetic variants in IRF6 and the risk of facial clefts: single-marker and haplotype-based analyses in a population-based case-control study of facial clefts in Norway. Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian pop...
common in complete genomics
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One form of this SNP, known as N991D, A3199G or Asn991Asp for the nonsynonymous change it produces in the BRCA2 protein, has been reported to represent an increased risk for malignant melanoma. In a Polish study of ~600 patients in comparison with ~3700 controls, the rs1799944 SNP was found to have an odds ratio of 1.8. Patients with the homozygous rs1799944(G;G) genotype were present in 0.32% of malignant melanoma cases vs. 0.13% of controls. In two Chinese families with histories of inherited breast cancer, A1093C (Asn289His) in exon 10 and A3199G (Asn991Asp, i.e. rs1799944) in exon 11 of BRCA2 were found occurring together, and they were not seen in pooled control DNA. Risk of non-Hodgkin lymphoma (NHL) in relation to germline variation in DNA repair and related genes. DNA-repair geneti...
common in clinvar
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rs4149584 is a SNP in the tumor necrosis factor receptor superfamily, member 1A TNFRSF1A gene. A large study (~5,000 patients) found two SNPs in the TNFRSF1A gene that each (independently) increase risk for multiple sclerosis, rs1800693 and rs4149584. This SNP, rs4149584, was less common but was associated with more risk; the odds ratio is reported as 1.6. [OMIM:?] [GWAS:Multiple sclerosis]
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
normal
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rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...
common in complete genomics
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rs505151 is a SNP, also known as E670G or 23968A>G, in the proprotein convertase subtilisin/kexin type 9 PCSK9 gene. rs505151(G) encodes the Gly (G), and rs505151(A) encodes the Glutamic acid (E). In a study of 506 European polygenic hypercholesterolemia patients, the rs505151(G) allele was found with increased frequency in men but not in women. rs505151 rs562556 show evidence of 'gain-of-function' mutations that are associated with higher LDL cholesterol levels. Longitudinal association of PCSK9 sequence variations with low-density lipoprotein cholesterol levels: the Coronary Artery Risk Development in Young Adults Study. The proprotein convertase subtilisin/kexin type 9 gene E670G polymorphism and serum lipid levels in the Guangxi Bai Ku Yao and Han populations. Genetic variability wi...
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T). Association between polymorphisms of the BRCA2 gene and clinical parameters in breast cancer.
common in complete genomics
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23andMe blog Influences QT interval [PharmGKB:Curated Associated with noise-induced hearing loss.] [OMIM:POTASSIUM CHANNEL, VOLTAGE-GATED, ISK-RELATED SUBFAMILY, MEMBER 1;]
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
common in clinvar
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rs2230288, also known as E326K or E365K, is a variation in the GBA gene which appears to be well tolerated; in other words, it is not associated with Gaucher disease. However, there is some evidence suggesting it is not a neutral polymorphism; instead, it appears to be a 'modifier' variant. [OMIM:?]
common in clinvar
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New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background. A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients. Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. A candidate gene association study of 77 polymorphisms in migraine. [OMIM:?]
common
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DNA-based methods in the immunohematology reference laboratory. Molecular basis of the Kell (K1) phenotype. Non-ABO Blood Groups [OMIM:KELL K/k BLOOD GROUP POLYMORPHISM]
Magnitude: 0
Frequency: 96.4%
Repute:Good
References:1
Frequency: 96.4%
Repute:Good
References:1
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
Magnitude: 0
Frequency: 96.7%
Repute:Good
References:1
Frequency: 96.7%
Repute:Good
References:1
Magnitude: 0
Frequency: 96.9%
Repute:Good
References:1
Frequency: 96.9%
Repute:Good
References:1
normal
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SNP rs2075291 represents a glycine to cysteine substitution at amino acid 185 of the APOA5 protein; it is also known as p.185Gly>Cys or c.553G>T. In both Chinese and non-Chinese Asians, the A allele (leading to the cysteine) is associated with higher risk for hypertriglyceridemia. The odds ratio is 4.45 (CI: 2.18-9.07, p<0.001). Heterozygosity was associated with a doubling of triglyceride levels, and all (11) rs2075291(A;A) homozygotes (as oriented relative to dbSNP, not as published) had severe hypertriglyceridemia (mean triglyceride level of 2292 +/- 447 mg/dl). [OMIM:?]
Magnitude: 0
Frequency: 97.3%
Repute:Good
References:1
Frequency: 97.3%
Repute:Good
References:1
common in clinvar
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[OMIM:PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MITOCHONDRIAL DNA DELETIONS, DIGENIC]
Magnitude: 0
Frequency: 98.1%
Repute:Good
References:1
Frequency: 98.1%
Repute:Good
References:1
common in clinvar
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[OMIM:MUSCULAR DYSTROPHY, CONGENITAL, 1C, WITH NEUROLOGIC ABNORMALITIES]
common
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[PharmGKB:Curated This study showed a highly significant association between a COMT haplotype of two functional SNPs (Ala72Ser and Val158Met) and aggressive behavior in schizophrenia.] [OMIM:SCHIZOPHRENIA, SUSCEPTIBILITY TO]
Magnitude: 0
Frequency: 98.2%
Repute:Bad
References:18
Frequency: 98.2%
Repute:Bad
References:18
normal Since the rare geno is good, this can be considered slightly bad
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rs11591147, also known as R46L, is a SNP in the PCSK9 gene. As early as 2006, the minor rs11591147(T) allele was reported to be associated with lower LDL cholesterol levels, and most studies since have found that this also correlates to a two to three fold reduced risk for both early- and late-onset cardiovascular events and disease. As part of a 9 SNP set studied in a meta-analysis totaling over 300,000 patients, rs11591147 was the SNP with the greatest effect on LDL-C and therefore cardiovascular risk reduction. The set of SNPs was as follows, ordered from strongest to least effect on coronary risk, and the allele shown is the one associated with reduced LDL-C levels along with the associated (or nearby) lipid metabolism gene: * rs11591147(T), PCSK9 * rs4420638(A), APOE * rs6511720(T), L...
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:3
Frequency: 98.2%
Repute:Good
References:3
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:1
Frequency: 98.2%
Repute:Good
References:1
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:4
Frequency: 98.2%
Repute:Good
References:4
common in complete genomics
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rs17110563, also known as Pro206Ser, is a SNP in the TPH2 gene. The minor allele of this SNP yielded an odds ratio of 4.8 (CI:1.6-14.8) for increased risk for bipolar disorder in a study of 883 Russian patients. [PharmGKB:Curated This variant has been reported to be associated with unipolar and bipolar depression in different populations.] [OMIM:TRYPTOPHAN HYDROXYLASE 2; TPH2]
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:10
Frequency: 98.2%
Repute:Good
References:10
normal
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rs41293463 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 841. The more common rs41293463(C) allele encodes Arg, while the rare rs41293463(T) allele encodes Trp; this SNP is also known as R841W. A 1996 study of 305 cases in Southern California of breast cancer and ovarian cancer found 3 cases carrying the rs1800709(T) allele. In all three cases, there was a strong family history of breast, ovarian, or other cancers, and family members showed a high concordance of cancer incidence with the presence of this SNP. However, the age of cancer onset was the same as for sporadic cases. The authors conclude that this SNP may explain around 1% (CI: 0-1.7%) of all breast and ovarian cancers, at least for this population. Note: this SNP is rather unlikely to ...
normal
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rs1800888, also known as Ile164, is a SNP in the beta 2 adrenergic receptor ADRB2 gene. The rs1800888(T) encodes the much rarer Ile allele. In a study of 330 patients undergoing percutaneous coronary intervention (PCI), patients carrying a rs1800888(T) allele showed a higher incidence of new acute myocardial infarction (17.5% vs. 4.5%, p = 0.001), new PCI (37.5% vs. 13.1%, p < 0.0001), and cardiac death (10% vs. 3.1%, p = 0.036). Regression analysis identified rs1800888(T) as an independent predictor of cardiac death (odds ratio 3.731, CI: 1.004 - 13.867, p = 0.049) and an overall major adverse cardiac event (odds ratio 4.1, CI: 1.945 - 8.640, p = 0.0001). A replication study was done on a population of 150 patients with peripheral artery disease. The presence of the rs1800888(T) allele...
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:2
Frequency: 98.2%
Repute:Good
References:2
common in complete genomics
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rs964201 is an A/G SNP located in the ASPM gene. The G-allele of this SNP as well as the A-allele of rs3762271 another SNP located in the ASPM gene and rs2442496 a SNP in the MCPH1 gene arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans. A comment is found at g2b2mh.
Magnitude: 0
Frequency: 98.3%
Repute:Good
References:2
Frequency: 98.3%
Repute:Good
References:2
Magnitude: 0
Frequency: 98.4%
Repute:Good
References:7
Frequency: 98.4%
Repute:Good
References:7
common in clinvar
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The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. 23andMe tests for SNPs in the MEFV gene that are associated with a recessive form of familial Mediterranean fever: * rs28940579, also known as V726A (risk allele G) * rs28940580, also known as M680I C>G (risk allele G) * rs28940578, also known as M694I (risk allele T) * rs3743930, also known as E148Q (risk allele G) * rs11466023, also known as P369S (risk allele A) * i4000406, also known as M694V (risk allele C) * i4000409, also known as A744S (risk allele A) * i4000403, also known as F479L (risk allele C) * i4000410, also known as R761H (risk allele T) * i40...
Magnitude: 0
Frequency: 98.4%
Repute:Good
References:2
Frequency: 98.4%
Repute:Good
References:2
normal
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A complex pattern of mutations involving rs17158558(T) and other mutations simultaneously occurring may - or with greater odds, actually, may not - lead to Hirschsprung disease. [OMIM:HIRSCHSPRUNG DISEASE]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:9
Frequency: 99.1%
Repute:Good
References:9
normal
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[PharmGKB:Curated This variant is associated with risk of pancreatitits for HIV-infected individuals.] [OMIM:PANCREATITIS, CHRONIC, SUSCEPTIBILITY TO]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:1
Frequency: 99.1%
Repute:Good
References:1
Typical BuChE
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rs1799807, also known as D70G, is a SNP in the BCHE gene. This SNP affects the structure, activity, and substrate specificity of the BuChE (butyrylcholinesterase) enzyme. [Cholinesterases and cholinesterase inhibitors, p. 48] The variant form, rs1799807(G), replaces aspartate with glycine at the secondary substrate/inhibitor binding site. This single base substitution yields the 'atypical' version of BChE. This version has a lower affinity for many substrates, including many Cholinesterase Inhibitors (CIs). A different cholinesterase (acetylcholinesterase, AChE) is an important component of neurotransmission by acetylcholine (ACh), terminating the action of ACh after it has been released during neurotransmission. BChE is found widely in the plasma and normally binds to CIs, protecting AChE...
common in clinvar
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omim notes that links this snp to Duchenne muscular dystrophy, but hapmap frequency makes that seem very unlikely. [OMIM:DUCHENNE MUSCULAR DYSTROPHY]
common in complete genomics
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
normal
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Although the rs26722(T) alllele is relatively rare, at least statistically it seems to be associated with darker eye, hair, and skin color, all other things being equal. A genomewide association study of skin pigmentation in a South Asian population. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Association of the SLC45A2 gene with physiological human hair colour variation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Genetic determinants of hair and eye colours in the Scottish and Danish populations. [OMIM:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
common in clinvar
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rs268, a SNP in the lipoprotein lipase LPL gene, has been linked to increased susceptibility to idiopathic venous thromboembolism. A study of 300+ individuals resulted in an odds ratio of 3.09 (CI: 1.56-6.09, p=0.001) for carriers of a rs268(G) allele. [OMIM:?] [GWAS:None]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:1
Frequency: 99.1%
Repute:Good
References:1
common in clinvar
(hide)
[PharmGKB:In-Depth Has been studied in association with long QT.] [OMIM:LONG QT SYNDROME 3, ACQUIRED, SUSCEPTIBILITY TO]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
(hide)
Several African-American rs10250779(T;T) homozygotes (as oriented in dbSNP) have been reported to experience intense muscle pain and cramps upon exercising. It is not known what percentage of such homozgyotes respond to exercise in this manner. Distribution and effects of nonsense polymorphisms in human genes. [OMIM:MYOPATHY DUE TO DEFICIENCY OF MUSCLE PHOSPHOGLYCERATE MUTASE]
common in clinvar
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[PharmGKB:Curated In a study of pediatric malaria treatments in Africa, patients with G6PD deficiency, as assessed by the G6PD:202G>A variant, showed a higher risk of severe anaemia following treatment with chlorproguanil-dapsone plus artesunate.] [OMIM:G6PD ASAHI]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:3
Frequency: 100.0%
Repute:Good
References:3
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:3
Frequency: 100.0%
Repute:Good
References:3
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
(hide)
This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C).
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
(hide)
This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C).
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in clinvar
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Cystic Fibrosis mutation [OMIM:VAS DEFERENS, CONGENITAL BILATERAL ABSENCE OF]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:7
Frequency: 100.0%
Repute:Good
References:7
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
(hide)
This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
common on affy axiom data
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Two novel pathogenic mitochondrial DNA mutations affecting organelle number and protein synthesis. Is the tRNA(Leu(UUR)) gene an etiologic hot spot? Mutational analysis of the mitochondrial 12S rRNA gene in Chinese pediatric subjects with aminoglycoside-induced and non-syndromic hearing loss. The role of selection in the evolution of human mitochondrial genomes.
normal risk
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A common SNP only in Asian populations, this SNP (also known as 1425G/A) and a close neighbor also in the PRKCH gene, rs3783799, have been associated with higher risk for subcortical silent brain infarction, a common form of stroke. In one study of ~1100 Japanese stroke patients, the odds ratio for carriers of the rs2230500(A) risk allele was reported as 1.40 (CI: 1.23-1.59, p=5x10e-7). A subsequent study reported the odds ratio for carriers of the (A) allele as 1.27 (CI: 1.09-1.48, p=0.0026) compared to individuals homozygous for rs2230500(G), based on studies of ~300 Japanese patients. rs2230500 (V374I) and rs9943582 were significantly associated with stroke Genetic association between the PRKCH gene encoding protein kinase Ceta isozyme and rheumatoid arthritis in the Japanese population...
common in clinvar
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Association of cholesteryl ester transfer protein genotypes with CETP mass and activity, lipid levels, and coronary risk. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients. TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population. [OMIM:CHOLESTEROL ESTER TRANSFER PROTEIN DEFICIENCY]
common in complete genomics
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NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:B-CELL NON-HODGKIN LYMPHOMA, SOMATIC]
common in clinvar
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Familial hypertrophic cardiomyopathy see also OMIM 160760.0002 [OMIM:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 1]
common in clinvar
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Familial hypertrophic cardiomyopathy see also OMIM 160760.0015 [OMIM:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 1]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in clinvar
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Identification of a novel Bardet-Biedl syndrome protein, BBS7, that shares structural features with BBS1 and BBS2. Genetic interaction of BBS1 mutations with alleles at other BBS loci can result in non-Mendelian Bardet-Biedl syndrome. [OMIM:?]
common in clinvar
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gnxp hair thickness for asians gnxp blog tooth shape among asians A picture of shovel shaped incisors is at http://www.flickr.com/photos/39602184@N02/3747590190/ [OMIM:ECTODYSPLASIN A RECEPTOR; EDAR]
normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
normal
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rs5742904, also known as R3527Q, is a SNP in the APOB apolipoprotein B gene. The risk allele is T according to 23andMe, which tests for this SNP in regard to familial hypercholesterolemia type B. In SNPedia, where we use the orientation as defined by dbSNP, the risk allele is rs5742904(A). For a clinical case discussion of this SNP, see 'Clinical Case 2' within Box 1 of . Familial Hypercholesterolemia Type B [OMIM:HYPERCHOLESTEROLEMIA DUE TO LIGAND-DEFECTIVE APOLIPOPROTEIN B100]
common in clinvar
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Regarding Homocystinuria, the I278T mutation has been associated with B6 responsiveness and a relatively mild clinical phenotype when homozygous. Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma. Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. A candidate gene association study of 77 polymorphisms in migraine. [PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The T variant of rs5742905 was associated with Spina Bifida in a transmission disequilibrium test. Study size: 610 families (329 trios, 281 duos) Study population/et...
normal
(hide)
rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Tests for th...
common in complete genomics
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[PharmGKB:In-Depth Has been studied in association with long QT.]
common in clinvar
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[PharmGKB:Curated In a family linkage study, rs846664 was shown to be significantly associated with risk for alcohol dependence. The risk allele appears at a much higher frequency in African Americans than in European Americans.] [OMIM:TASTE RECEPTOR, TYPE 2, MEMBER 16; TAS2R16]
common in clinvar
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GPX1 Pro198Leu polymorphism, interactions with smoking and alcohol consumption, and risk for lung cancer. Gene x Gene interaction between MnSOD and GPX-1 and breast cancer risk: a nested case-control study. Genetic association of glutathione peroxidase-1 with coronary artery calcification in type 2 diabetes: a case control study with multi-slice computed tomography. Do genetic factors protect for early onset lung cancer? A case control study before the age of 50 years. A prospective study of genetic polymorphism in MPO, antioxidant status, and breast cancer risk. Oxidative response gene polymorphisms and risk of adult brain tumors. The Mn-superoxide dismutase single nucleotide polymorphism rs4880 and the glutathione peroxidase 1 single nucleotide polymorphism rs1050450 are associated with ...
G6PD Type B
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23andMe blog G6PD Deficiency [PharmGKB:Curated Causes a slight decrease in G6PD activity.] [OMIM:G6PD A+]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
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According to 23andMe, only the A allele at rs12948217 confers risk to Canavan disease. A person with the CC, CT, or TT alleles is not a carrier; someone with the AC or AT alleles is a carrier; and people with two AA alleles are affected with the disease. [OMIM:[[Canavan disease]]]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs17847577 represents the most common WRN mutation seen in Caucasians as well as all other non-Japanease populations. See also: OMIM604611.0006 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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This SNP, a variant in the CHEK2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). rs17879961 one of 3 SNPs associated with increased risk of lung cancer [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
common in complete genomics
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Alpha 1-antitrypsin deficiency, emphysema, and liver disease. Genetic basis and strategies for therapy. Molecular analysis of the heterogeneity among the P-family of alpha-1-antitrypsin alleles. [OMIM:?]
common in complete genomics
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rs1804197, a SNP in the adenomatous polyposis of the colon APC gene, is associated with autism . Although many SNPs have been found in this gene in association with (successful) hunts for mutations predisposing individuals to colon cancers, this previously unidentified SNP is located in the 3' untranslated portion of the gene. Also in conjunction with a common four-SNP haplotype (TGAG for rs2229992, rs42427, rs459552, and rs465899), this SNP is reported to be associated with Asperger's sydrome in the Swedish population studied. [OMIM:?]
common in complete genomics
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rs1805006, known as Asp84Glu or D84E, is one of several SNPs in the MC1R gene associated with higher risk of melanoma. The risk allele is rs1805006(A), compared with the wild-type rs1805006(C) allele. Allelic odds ratio for pale skin(P-value)=5.19(<1.0e-5)MC1R*D84E rs1805006 http://genepi.qimr.edu.au/contents/p/staff/Duffyetal_JID_520-528Jan10.pdf See also OMIM 155555.0003 [OMIM:?]
common in complete genomics
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Common candidate gene variants are associated with QT interval duration in the general population. In silico investigations on functional and haplotype tag SNPs associated with congenital long QT syndromes (LQTSs). Pyrrolo(1,4)benzodiazepine antitumor antibiotics. In vitro interaction of anthramycin, sibiromycin and tomaymycin with DNA using specifically radiolabelled molecules. A common polymorphism associated with antibiotic-induced cardiac arrhythmia. Screening for mutations and polymorphisms in the genes KCNH2 and KCNE2 encoding the cardiac HERG/MiRP1 ion channel: implications for acquired and congenital long Q-T syndrome. DHPLC analysis of potassium ion channel genes in congenital long QT syndrome. Ethnic differences in cardiac potassium channel variants: implications for genetic susc...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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23andMe blog The T version of rs11591147 and the A version of rs28362286 have both been associated with decreased LDL levels. Each copy of these variants leads to lower LDL cholesterol. Longitudinal association of PCSK9 sequence variations with low-density lipoprotein cholesterol levels: the Coronary Artery Risk Development in Young Adults Study. [OMIM:LOW DENSITY LIPOPROTEIN CHOLESTEROL, LOW PLASMA LEVELS OF]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs28897672 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 61. The more common rs28897672(T) allele encodes Cys, while the rare rs28897672(G) allele encodes Gly; this variation is also known as Cys61Gly or C61G. A study of 66 Polish families affected with breast cancer or ovarian cancer, often diagnosed at a relatively young age (< 50 years old), screened for BRCA1 mutations by sequencing. The C61G mutation accounted for 20% of the identified mutations in this group of families. * See also Omim 113705.0002 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28897696, also known as A1708E, is a SNP in the BRCA1 gene. The far more common (C) allele encodes the amino acid alanine (A), while the very rare (A) allele encodes glutamic acid (E). An analysis of sequence variants of unknown clinical significance in the BRCA1 and BRCA2 genes concluded that this SNP was among the top 10 (over both genes) likely to lead to breast cancer, with a calculated odds of over 1,000:1 against this just being a spurious association. Although the clinical importance has not been proven, this may still be of use for genetic counseling.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28897756, also known as P3039P or 9345G/A, is a SNP in the breast cancer 2 BRCA2 gene. The rare rs28897756(A) allele has been linked to increased risk for breast cancer in some Dutch families.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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Allelic heterogeneity at the serotonin transporter locus (SLC6A4) confers susceptibility to autism and rigid-compulsive behaviors. Enhanced activity of human serotonin transporter variants associated with autism. Characterization of a functional polymorphism in the 3' UTR of SLC6A4 and its association with drinking intensity. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0009 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in complete genomics
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rs28929474, also known as Glu342Lys as well as E366K, is a SNP in the serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 gene. This SNP is the one most frequently leading, when homozygous, to the complications of alpha-1 antitrypsin deficiency and the associated high risk of emphysema and liver disease. Between 1 - 2% of US Caucasians are thought to be (heterozygous) carriers for this SNP, leading some associations, like the Alpha-1 Foundation, to call for mass carrier screening. * 23andMe blog rs28929474(T) increases odds of liver disease in cystic fibrosis patients by 4.17 times. (T;T) at both copies of this SNP causes alpha-1 antitrypsin deficiency; note use of opposite strand nomenclature by this company. finds no association between rs28929474...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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rs28931568 is a SNP representing an amino acid change in the SERPINA1 gene, which encodes alpha-1-antitrypsin (AAT). Carriers of two rs28931568(A) alleles, i.e. homozygotes, are at high risk for emphysema based on the finding of this variant in an affected African-American family. [OMIM:PI M(MINERAL SPRINGS)]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
(hide)
rs28931569 is a SNP representing an amino acid change in the SERPINA1 gene, which encodes alpha-1-antitrypsin (AAT). Carriers of two rs28931569(C) alleles, i.e. homozygotes, are at high risk for emphysema . [OMIM:PI M(PROCIDA)]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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wikipedia has a fairly detailed article on this particular variant [OMIM:APOLIPOPROTEIN A-I (MILANO)]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:PILOMATRICOMA, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 3]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:PARATHYROID ADENOMA, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148041.0002 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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[OMIM:ECTODERMAL DYSPLASIA, ANHIDROTIC, WITH T-CELL IMMUNODEFICIENCY, AUTOSOMAL DOMINANT]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:GLIOBLASTOMA, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:GASTRIC CANCER, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:OVARIAN CARCINOMA, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:GASTRIC CANCER, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
(hide)
In silico investigations on functional and haplotype tag SNPs associated with congenital long QT syndromes (LQTSs). [PharmGKB:Curated In one family, this mutation is associated with Jervell and Lange-Nielsen syndrome (JLNS), along with an Asp76Asn mutation.] [OMIM:JERVELL AND LANGE-NIELSEN SYNDROME]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Transmission of spongiform encephalopathy from a familial Creutzfeldt-Jakob disease patient of Jewish Libyan origin carrying the PRNP codon 200 mutation. Familial Creutzfeldt-Jakob disease (codon 200 mutation) with supranuclear palsy. Familial Creutzfeldt-Jakob disease in Chile is associated with the codon 200 mutation of the PRNP amyloid precursor gene on chromosome 20. Genetic and environmental factors determining the development of Creutzfeldt-Jakob disease in Libyan Jews. The risk of developing Creutzfeldt-Jakob disease in subjects with the PRNP gene codon 200 point mutation. Age and origin of the PRNP E200K mutation causing familial Creutzfeldt-Jacob disease in Libyan Jews. [OMIM:CREUTZFELDT-JAKOB DISEASE]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar common
(hide)
(T;T) has a moderate change in BCHE activity according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
(T;T) abolishes catalytic activity in BCHE according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:11
Repute:Good
References:11
common in clinvar
(hide)
[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Different RYR1 variants are associated with significant differences in in vitro contracture tests (IVCT) and creatine kinase (CK) phenotypes; more specifically, the variants p.R163C, p.R2163H (rs28933999 G to A), p.R2435H (rs28933396 G to A), and p.T4826I were significantly associated with a more severe form of each quantitative phenotype Study size: 450. Study population/ethnicity: Malignant hyperthermia -susceptible individuals (Caucasians).] [OMIM:CENTRAL CORE DISEASE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
[Association of the polymorphisms of sodium transport related genes with essential hypertension]. [OMIM:MIGRAINE, FAMILIAL HEMIPLEGIC, 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Leigh syndrome is more common in some French-Canadian populations. [OMIM:LEIGH SYNDROME DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
Familial hypertrophic cardiomyopathy see also OMIM 188840.0001 [OMIM:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 9]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:THYROID CARCINOMA, FOLLICULAR, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:THYROID HORMONE RESISTANCE, GENERALIZED, AUTOSOMAL DOMINANT]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:CEREBRAL ARTERIOPATHY, AUTOSOMAL DOMINANT, WITH SUBCORTICAL INFARCTS AND LEUKOENCEPHALOPATHY]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Germline p53 Mutation in a Case of Li-Fraumeni Syndrome Presenting Gastric Cancer. A germline missense mutation CGT (Arg, wild type) to CAT (His) substitution at codon 273 of the p53 gene, causing Li-Fraumeni Syndrome with a gastric cancer in a Japanese. PCR direct sequencing analysis revealed a germline missense mutation in exon 8, causing a substitution of CAT (His) for CGT (Arg). [OMIM:LI-FRAUMENI SYNDROME]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
rs28934578, also known as 721G>A, R175H and Arg175His, is a SNP in the p53 TP53 tumor suppressor gene. The rare rs28934578(A) allele is associated with predisposition to cancer in the form of Li-Fraumeni syndrome 1. [OMIM:LI-FRAUMENI SYNDROME 1]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
[OMIM:APPARENT MINERALOCORTICOID EXCESS, HYPERTENSION DUE TO]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
[OMIM:APPARENT MINERALOCORTICOID EXCESS, HYPERTENSION DUE TO]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
[OMIM:APPARENT MINERALOCORTICOID EXCESS, HYPERTENSION DUE TO]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
[Effect of the trace element supply on element dependent enzymes in man]. Exon scanning of the entire TSC2 gene for germline mutations in 40 unrelated patients with tuberous sclerosis. Mutational analysis of TSC1 and TSC2 genes in Japanese patients with tuberous sclerosis complex. TSC1 and TSC2 mutations in tuberous sclerosis, the associated phenotypes and a model to explain observed TSC1/ TSC2 frequency ratios. Mutation and polymorphism analysis of TSC1 and TSC2 genes in Indian patients with tuberous sclerosis complex. Precise prenatal diagnosis of tuberous sclerosis by sequencing the TSC2 gene. Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States. [OMIM:TUBEROUS SCLEROSIS 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
(hide)
X-linked recessive chondrodysplasia punctata: spectrum of arylsulfatase E gene mutations and expanded clinical variability. [OMIM:CHONDRODYSPLASIA PUNCTATA 1, X-LINKED RECESSIVE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:IMMUNODYSREGULATION, POLYENDOCRINOPATHY, AND ENTEROPATHY, X-LINKED]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Prevalence of fabry disease in a cohort of 508 unrelated patients with hypertrophic cardiomyopathy. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
A novel DKC1 mutation, severe combined immunodeficiency (T+B-NK- SCID) and bone marrow transplantation in an infant with Hoyeraal-Hreidarsson syndrome. [OMIM:HOYERAAL-HREIDARSSON SYNDROME]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:COLON CANCER, SOMATIC]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Analysis of body height in 829 patients with different forms of testicular pathology. Atrial form and function: lessons from human molecular genetics. Progressive AV-block and anomalous venous return among cardiac anomalies associated with two novel missense mutations in the CSX/NKX2-5 gene. Two novel frameshift mutations in NKX2.5 result in novel features including visceral inversus and sinus venosus type ASD. Phenotypes with GATA4 or NKX2.5 mutations in familial atrial septal defect. NKX2.5 mutations in patients with non-syndromic congenital heart disease. [OMIM:TETRALOGY OF FALLOT]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Homozygous mutations in caveolin-3 cause a severe form of rippling muscle disease. [OMIM:RIPPLING MUSCLE DISEASE 2]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:PULMONARY ARTERIAL HYPERTENSION, HEREDITARY HEMORRHAGIC TELANGIECTASIA-RELATED]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:NON-HODGKIN LYMPHOMA, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:HYPOTHYROIDISM, ATHYROIDAL, WITH SPIKY HAIR AND CLEFT PALATE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
[OMIM:ERYTHROKERATODERMIA VARIABILIS, AUTOSOMAL RECESSIVE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:CARDIOENCEPHALOMYOPATHY, FATAL INFANTILE, DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:CARDIOENCEPHALOMYOPATHY, FATAL INFANTILE, DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:PERIVENTRICULAR HETEROTOPIA WITH MICROCEPHALY, AUTOSOMAL RECESSIVE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
[OMIM:BLEPHAROPHIMOSIS, PTOSIS, AND EPICANTHUS INVERSUS, TYPE I]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 6]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 6]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:ESOPHAGEAL SQUAMOUS CELL CARCINOMA, SOMATIC]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
Familial hypertrophic cardiomyopathy see also OMIM 602743.0004 [OMIM:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, WITH WOLFF-PARKINSON-WHITE SYNDROME]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:GLUTATHIONE SYNTHETASE DEFICIENCY OF ERYTHROCYTES, HEMOLYTIC ANEMIA DUE TO]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:TRIGLYCERIDE STORAGE DISEASE WITH IMPAIRED LONG-CHAIN FATTY ACID]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:POLYCYSTIC LIPOMEMBRANOUS OSTEODYSPLASIA WITH SCLEROSING LEUKOENCEPHALOPATHY]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Two hypoxia sensor genes and their association with symptoms of acute mountain sickness in Sherpas. [3 cases of fenestration of the vertebral artery]. Cellular proteins that bind the von Hippel-Lindau disease gene product: mapping of binding domains and the effect of missense mutations. Renal cell carcinomas in trichloroethene (TRI) exposed persons are associated with somatic mutations in the von Hippel-Lindau (VHL) tumour suppressor gene. Disruption of oxygen homeostasis underlies congenital Chuvash polycythemia. Congenital disorder of oxygen sensing: association of the homozygous Chuvash polycythemia VHL mutation with thrombosis and vascular abnormalities but not tumors. Role of VHL gene mutation in human cancer. [OMIM:POLYCYTHEMIA, CHUVASH TYPE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 4]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Prenatal testing for late infantile neuronal ceroid lipofuscinosis. [Tripeptidyl peptidase 1 deficiency in neuronal ceroid lipofuscinosis. A novel mutation]. [OMIM:CEROID LIPOFUSCINOSIS, NEURONAL, 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. 23andMe tests for SNPs in the MEFV gene that are associated with a recessive form of familial Mediterranean fever: * rs28940579, also known as V726A (risk allele G) * rs28940580, also known as M680I C>G (risk allele G) * rs28940578, also known as M694I (risk allele T) * rs3743930, also known as E148Q (risk allele G) * rs11466023, also known as P369S (risk allele A) * i4000406, also known as M694V (risk allele C) * i4000409, also known as A744S (risk allele A) * i4000403, also known as F479L (risk allele C) * i4000410, also known as R761H (risk allele T) * i40...
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in clinvar
(hide)
The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. 23andMe tests for SNPs in the MEFV gene that are associated with a recessive form of familial Mediterranean fever: * rs28940579, also known as V726A (risk allele G) * rs28940580, also known as M680I C>G (risk allele G) * rs28940578, also known as M694I (risk allele T) * rs3743930, also known as E148Q (risk allele G) * rs11466023, also known as P369S (risk allele A) * i4000406, also known as M694V (risk allele C) * i4000409, also known as A744S (risk allele A) * i4000403, also known as F479L (risk allele C) * i4000410, also known as R761H (risk allele T) * i40...
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in clinvar
(hide)
The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. 23andMe tests for SNPs in the MEFV gene that are associated with a recessive form of familial Mediterranean fever: * rs28940579, also known as V726A (risk allele G) * rs28940580, also known as M680I C>G (risk allele G) * rs28940578, also known as M694I (risk allele T) * rs3743930, also known as E148Q (risk allele G) * rs11466023, also known as P369S (risk allele A) * i4000406, also known as M694V (risk allele C) * i4000409, also known as A744S (risk allele A) * i4000403, also known as F479L (risk allele C) * i4000410, also known as R761H (risk allele T) * i40...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar common for Caucasians on the 23andme platform
(hide)
[OMIM:ALBINISM, OCULOCUTANEOUS, TYPE IA]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:PALMOPLANTAR KERATODERMA, EPIDERMOLYTIC, WITH KNUCKLE PADS]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, CYTOCHROME b-NEGATIVE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
(A;A) familial hypercholesterolemia 23% frequency among Afrikaners 1.5% frequency among Dutch [OMIM:FH AFRIKANER 2]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
[OMIM:ATRIOVENTRICULAR SEPTAL DEFECT, SUSCEPTIBILITY TO, 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
(hide)
[OMIM:ATRIOVENTRICULAR SEPTAL DEFECT, SUSCEPTIBILITY TO, 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Distribution and effects of nonsense polymorphisms in human genes. [OMIM:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
[OMIM:PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL DOMINANT, 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
(hide)
rs33930165 is a relatively rare SNP found in the beta hemoglobin HBB gene, adjacent to the well-known SNP associated with malarial resistance (rs334). This SNP gives rise to the 'Hb C', or hemoglobin C, form of hemoglobin as the HBB forms are commonly named. It is found primarily in a subset of West Africa. rs33930165 is associated with increased malarial resistance, yet without giving rise to sickle cell anemia. A study of 4,000+ individuals in Burkina Faso found that rs33930165(A;G) heterozygotes had a 29% reduction in risk of clinical malaria (p = 0.0008), and rs33930165(C;C) homozygotes had a 93% reduction (p = 0.0011). [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
(hide)
rs33950507 is a SNP found in the beta hemoglobin HBB gene, not far from the well-known SNP associated with malarial resistance (rs334, Hb S). This SNP gives rise to the 'Hb E', or hemoglobin E, form of hemoglobin as the HBB forms are commonly named. It is found primarily in Southeast Asia. rs33950507(A) is associated with somewhat increased malarial resistance, and in homozygous (A;A) state, with mild hypochromic microcytic anemia. Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:N-ACETYLGLUCOSAMINE-1-PHOSPHOTRANSFERASE, ALPHA/BETA SUBUNITS; GNPTAB]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
References:1
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/ A new frameshift beta zero-thalassemia mutation (codons 27-28 +C) found in a Chinese family. The spectrum of beta-thalassemia mutations in Taiwan: identification of a novel frameshift mutation. The spectrum of beta-thalassemia genes in China and Southeast Asia. beta-Thalassemia in Chinese: use of in vivo RNA analysis and oligonucleotide hybridization in systematic characterization of molecular defects. Molecular basis and haematological characterization of beta-thalassaemia major in Taiwan, with a mutation of IVS-1 3' end TAG-->GAG in a Chinese patient.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
(hide)
rs34612342, also known as Tyr179Cys, is one of the two most common pathogenic mutations in the MUTYH gene. The normal allele, encoding the tyrosine, is rs34612342(A), while rs34612342(G) is the risk allele. [Mutation nomenclature according to Genbank accession number NM_001128425.1 c.536A>G, p.Tyr179Cys; alternative numbering can lead to this SNP also being called Tyr151Cys, Tyr152Cys, Tyr165Cys, or Tyr176Cys.] Germline bi-allelic mutations in the MUTYH gene increase the risk of developing multiple adenomatous polyps and colorectal cancer. [OMIM:?]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
(hide)
First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Variations in the NBN/NBS1 gene and the risk of breast cancer in non-BRCA1/2 French Canadian families with high risk of breast cancer. [OMIM:?]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
(hide)
In perfect contrast to another SNP also within the LRRK2 gene, rs34637584, this SNP, rs34778348, is not found in Caucasian populations but is found in Asian populations. A case-control study of 989 Chinese subjects concluded that the odds ratio for Parkinson's disease was 2.1 for rs34778348(A) carriers (CI: 1.1-3.9, p = 0.014). This SNP was estimated to account for 4% of all Parkinson cases in this population. 23andMe blog Parkinson's disease [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2] [GWAS:None]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
Mutations of the cardiac ryanodine receptor (RyR2) gene in familial polymorphic ventricular tachycardia. Identification of mutations in the cardiac ryanodine receptor gene in families affected with arrhythmogenic right ventricular cardiomyopathy type 2 (ARVD2). Genomics, heart failure and sudden cardiac death. Systematic assessment of patients with unexplained cardiac arrest: Cardiac Arrest Survivors With Preserved Ejection Fraction Registry (CASPER). The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
(hide)
Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Cone cGMP-gated channel mutations and clinical findings in patients with achromatopsia, macular degeneration, and other hereditary cone diseases. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:9
Repute:Good
References:9
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
(hide)
Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal hearing
(hide)
hereditary non-syndromic sensorineural deafness Connexin mutations and hearing loss. Novel mutations in the connexin 26 gene (GJB2) that cause autosomal recessive (DFNB1) hearing loss. Connexin mutations in deafness. Autosomal recessive nonsyndromic neurosensory deafness at DFNB1 not associated with the compound-heterozygous GJB2 (connexin 26) genotype M34T/167delT. Genetic analysis of the connexin-26 M34T variant: identification of genotype M34T/M34T segregating with mild-moderate non-syndromic sensorineural hearing loss. GJB2 mutations and degree of hearing loss: a multicenter study. M34T and V37I mutations in GJB2 associated hearing impairment: evidence for pathogenicity and reduced penetrance. A multicenter study of the frequency and distribution of GJB2 and GJB6 mutations in a large N...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
(hide)
Macrophage activation syndrome in 13 children with systemic-onset juvenile idiopathic arthritis. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
(hide)
rs36053993, also known as Gly396Asp, is one of the two most common pathogenic mutations in the MUTYH gene. The risk allele is rs36053993(A), as oriented in accordance with dbSNP. (Mutation nomenclature according to Genbank accession number NM_001128425.1 c.1187G>A, p.Gly396Asp; numbering differences can lead to alternative designations including Gly368Asp, Gly369Asp, Gly382Asp, or Gly393Asp.) People with two copies of a single mutation in the MUTYH gene are at higher risk of developing multiple adenomatous polyps and colorectal cancer. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:10
Repute:Good
References:10
common in complete genomics
(hide)
[PharmGKB:Curated in vitro studies showed cisapride has same sensitivity for WT and this varian]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
(hide)
rs41293455 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 1443. The more common rs41293455(C) allele encodes Arg, while the rare rs41293455(T) allele encodes a stop codon. Another variant, rs41293455(G), encodes a Gly. A well known study published in 1994 looked at 50 family pedigrees with breast cancer and ovarian cancer susceptibility, discovering what they believed were eight putative disease-causing mutations (four frameshifts, two nonsense mutations) and an additional two missense mutations. rs41293455 was one of these variants. * See also Omim 113705.0016 * See also Omim 113705.0017 [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Also known as Lys224Arg, G allele is associated with Dopa-Responsive Dystonia. Dystonia with motor delay in compound heterozygotes for GTP-cyclohydrolase I gene mutations. Dopa-responsive dystonia in British patients: new mutations of the GTP-cyclohydrolase I gene and evidence for genetic heterogeneity. Autosomal dominant GTP-CH deficiency presenting as a dopa-responsive myoclonus-dystonia syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
(hide)
rs41309764, also known as R1108X, is a SNP in the NOTCH1 gene. The common allele is rs41309764(C), while the rare rs41309764(T) allele encodes the variant. A normal human heart contains three valves. Carriers of one rs41309764(T) allele, such as Arnold Schwarzenegger, will develop an early developmental defect in the aortic valve leading to a bicuspid aortic valve, and without treatment, they are prone to progressive aortic valve disease in their later life due to calcification. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
(hide)
Folliculin mutations are not associated with severe COPD. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common
(hide)
This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an Apo-ε4 allele. The Apo-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between the...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Lidocaine-induced Brugada syndrome phenotype linked to a novel double mutation in the cardiac sodium channel. An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing. [OMIM:?]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Three independent mutations in the TSC2 gene in a family with tuberous sclerosis. [OMIM:?]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Novel TSC2 mutation in a patient with pulmonary tuberous sclerosis: lack of loss of heterozygosity in a lung cyst. Mutational analysis of TSC1 and TSC2 genes in Japanese patients with tuberous sclerosis complex. [OMIM:?]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
(hide)
[OMIM:5,10-@METHYLENETETRAHYDROFOLATE REDUCTASE; MTHFR]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
In silico investigations on functional and haplotype tag SNPs associated with congenital long QT syndromes (LQTSs). Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodium channel gene (SCN5A). Sodium channel mutations and susceptibility to heart failure and atrial fibrillation. An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing. Mechanistic links between Na+ channel (SCN5A) mutations and impaired cardiac pacemaking in sick sinus syndrome. Multiple loss-of-function mechanisms contribute to SCN5A-related familial sick sinus syndrome. [OMIM:?]
normal
(hide)
rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
common in clinvar
(hide)
rs5030868 is SNP located on the X-Chromosome associated with moderate to severe Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency. Often referred to as the “Mediterranean variant”, the 563C->T mutation encodes a non-synonymous Serine to Phenylalanine substitution at Amino Acid position 188 (S188F) resulting in reduced catalytic efficiency and stability G6PD . In red blood cells, G6PD acts as the primary electron source for reactions that neutralize reactive oxygen species; thus the red blood cells of G6PD deficient individuals are especially susceptible to damage from oxidative stress . The Mediterranean variant of G6PD has been associated with acute hemolytic anemia induced by the ingestion of fava beans, glibenclamide, primaquine, dapsone, and Aspirin among others. <br><br&...
normal
(hide)
rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
(hide)
rs55770810, also known as R1699W, is a SNP in the BRCA1 gene. The more common (C) allele encodes the amino acid arginine (R), while the rare (T) allele encodes a tryptophan (W). An analysis of sequence variants of unknown clinical significance in the BRCA1 and BRCA2 genes concluded that this SNP was among the top 10 (over both genes) likely to lead to breast cancer, with a calculated odds of over 1,000:1 against this just being a spurious association. Although the clinical importance has not been proven, this may still be of use for genetic counseling.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
The contribution of USH1C mutations to syndromic and non-syndromic deafness in the UK. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
(hide)
DNA-based methods in the immunohematology reference laboratory. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
(hide)
This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148041.0004 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
(hide)
This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0007 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
(hide)
This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0006 [OMIM:?]
common in clinvar
(hide)
Association of warfarin dose with genes involved in its action and metabolism.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Transcriptional control of SLC26A4 is involved in Pendred syndrome and nonsyndromic enlargement of vestibular aqueduct (DFNB4). Hypo-functional SLC26A4 variants associated with nonsyndromic hearing loss and enlargement of the vestibular aqueduct: genotype-phenotype correlation or coincidental polymorphisms? The c.-103T>C variant in the 5'-UTR of SLC26A4 gene: a pathogenic mutation or coincidental polymorphism? [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
(hide)
This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148041.0003 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
DERMATOPATHIA PIGMENTOSA RETICULARIS Studying a family from the United States with the diagnosis of dermatopathia pigmentosa reticularis (DPR; 125595), first reported by Heimer et al. (1992), Lugassy et al. (2006) demonstrated a heterozygous C-to-A transversion at cDNA position 54 of KRT14, resulting in the nonsense mutation cys 18 to ter (C18X). [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Mutation analysis of the MECP2 gene in patients of Slavic origin with Rett syndrome: novel mutations and polymorphisms. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Alternative splicing suggests extended function of PEX26 in peroxisome biogenesis. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
A spectrum of ABCC6 mutations is responsible for pseudoxanthoma elasticum. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
Experimental immune glomerulonephritis induced in the rat by mercuric chloride. Systematic analysis of hMSH2 and hMLH1 in young colon cancer patients and controls. Bethesda guidelines: relation to microsatellite instability and MLH1 promoter methylation in patients with colorectal cancer. Clinicopathological and molecular genetic analysis of 4 typical Chinese HNPCC families. Identification and survival of carriers of mutations in DNA mismatch-repair genes in colon cancer. Switching from tacrolimus to sirolimus halts the appearance of new sebaceous neoplasms in Muir-Torre syndrome.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Arrhythmogenic right ventricular cardiomyopathy type 5 is a fully penetrant, lethal arrhythmic disorder caused by a missense mutation in the TMEM43 gene. [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Mutations in a gene encoding an ABC transporter cause pseudoxanthoma elasticum. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Bad
References:0
Repute:Bad
References:0
normal
(hide)
In APP source Detected in 1 patient with 2 ischemic strokes and myocardial infarction. No family history; no amyloid deposition. The variant also makes developing Alzheimer's disease four times less likely across all age groups. 'It confers extraordinarily strong protection,' said Stefansson. source http://www.decodeyou.com/decode-genetics-discovers-mutation-conferring-protection-against-alzheimers-disease-and-cognitive-decline-in-elderly/ http://blog.personalgenomes.org/2012/08/01/the-predominant-variant-of-the-app-gene-greatly-increases-risk-for-alzheimers-disease-and-cognitive-decline/
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
(hide)
Mutations in GDF6 are associated with vertebral segmentation defects in Klippel-Feil syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Characteristics of frontotemporal dementia patients with a Progranulin mutation. Progranulin mutations in primary progressive aphasia: the PPA1 and PPA3 families. Clinicopathologic correlation in PGRN mutations. Phenotypic variability associated with progranulin haploinsufficiency in patients with the common 1477C-->T (Arg493X) mutation: an international initiative. Distinct genetic forms of frontotemporal dementia. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:9
Repute:Good
References:9
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Ankyrin-B mutation causes type 4 long-QT cardiac arrhythmia and sudden cardiac death. A cardiac arrhythmia syndrome caused by loss of ankyrin-B function. Dysfunction in ankyrin-B-dependent ion channel and transporter targeting causes human sinus node disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Caveolin-3 in muscular dystrophy. Mutations in the caveolin-3 gene: When are they pathogenic? Molecular and muscle pathology in a series of caveolinopathy patients. CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Caveolin-3 in muscular dystrophy. Mutations in the caveolin-3 gene: When are they pathogenic? CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome. Novel mechanism for sudden infant death syndrome: persistent late sodium current secondary to mutations in caveolin-3. Caveolin-3 T78M and T78K missense mutations lead to different phenotypes in vivo and in vitro. CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome. Prevalence of long-QT syndrome gene variants in sudden infant death syndrome. Novel mechanism for sudden infant death syndrome: persistent late sodium current secondary to mutations in caveolin-3. Caveolin-3 T78M and T78K missense mutations lead to...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Six new mutations in the ornithine transcarbamylase gene detected by single-strand conformational polymorphism. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
[OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A). [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Human beta-galactosidase gene mutations in morquio B disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Mutations in acid beta-galactosidase cause GM1-gangliosidosis in American patients. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Impaired elastic-fiber assembly by fibroblasts from patients with either Morquio B disease or infantile GM1-gangliosidosis is linked to deficiency in the 67-kD spliced variant of beta-galactosidase. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 cause Aicardi-Goutieres syndrome at the AGS1 locus. Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 are associated with systemic lupus erythematosus. Clinical and molecular phenotype of Aicardi-Goutieres syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
Osteogenesis imperfecta due to recurrent point mutations at CpG dinucleotides in the COL1A1 gene of type I collagen. Substitution of arginine for glycine at position 154 of the alpha 1 chain of type I collagen in a variant of osteogenesis imperfecta: comparison to previous cases with the same mutation. Consortium for osteogenesis imperfecta mutations in the helical domain of type I collagen: regions rich in lethal mutations align with collagen binding sites for integrins and proteoglycans. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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more likely to gain weight if taking olanzapine
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and o...
common in clinvar
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The ancestral allele is C. Association of ApoE genetic variants with obstructive sleep apnea in children. Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes. [OMIM:HYPERLIPOPROTEINEMIA, TYPE III, ASSOCIATED WITH APOE2]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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Mutations in a gene encoding a novel SH3/TPR domain protein cause autosomal recessive Charcot-Marie-Tooth type 4C neuropathy. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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'After evaluating over 6,000 cases and 6,000 controls, there is little evidence of a role for the SRD5A2 A49T (i.e. rs9282858) variant in prostate cancer risk.' [OMIM:STEROID 5-ALPHA-REDUCTASE POLYMORPHISM]
average
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rs9332964 is a nonsynonymous change known as R227Q in the SRD5A2 gene. The SRD5A2 gene encodes steroid 5-alpha-reductase, an enzyme which catalyzes the conversion of testosterone in the body. Polymorphisms in SRD5A2 have been implicated in several disorders of male sexual development such as micropenis. The homozygous rs9332964(A;A) genotype has been observed in several Japenese males with micropenis. [OMIM:MICROPENIS]
generally non-European, but if European, 7x more likely to have black hair
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pi...
common in clinvar
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rs523349 is a SNP in the steroid-5-alpha-reductase SRD5A2 gene; it is also known as V89L. In a study of a total of 1,466 Caucasian cases of ovarian cancer, the rs523349(G) allele showed a significant trend of increasing risk of ovarian cancer per rare allele (p = 0.00002). showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
common in clinvar
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rs7493, also known as Ser311Cys, is a missense SNP in the paraoxonase 2 (PON2) gene. A study has shown that inheriting the Cys version encoded by the corresponding SNP results in impaired (lower) lactonase activity; this may (or may not) lead to problems with innate immunity, atherosclerosis, and other diseases. [OMIM:?]
common
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SNP rs2273535, also known as F31I or Phe31Ile, has been associated with increased risk for several cancers, in most cases when individuals are homozgyous for the risk allele, rs2273535(T), as oriented to the dbSNP entry. A meta-analysis of almost 10,000 cases of breast, colon, ovarian, prostate, lung, esophageal and non-melanoma skin cancer, compared to an equal number of Caucasian controls, determined the following risks (i.e., odds ratios, OR) : *For colorectal cancer: OR for homozygotes of 1.5 (CI: 1.14-1.99) *For breast cancer: OR for homozygotes of 1.35 (CI: 1.12-1.64) *For any of the cancer types studied: OR for heterozygotes of 1.10 (CI: 1.03-1.18), OR for homozygotes of 1.40 (CI: 1.22-1.59) In a Chinese population, breast cancer risk for rs2273535(T;T) homozygotes compared to the o...
common in clinvar
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DNA-based methods in the immunohematology reference laboratory. [OMIM:?]
common in complete genomics appears to be common on the 23andMe platform
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[OMIM:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
common on affy axiom data
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rs1045485, also known as D302H, is a SNP in the caspase-8 CASP8 gene. Several large studies indicate that the (C) allele of this SNP, located in exon 10 of the CASP8 gene, may reduce the risk of breast cancer in a dose dependent manner. The odds ratio is 0.89 for (C;G) and 0.74 for (C;C) carriers. article cancergenetics A 4-SNP haplotype including rs1045485 was significantly associated with breast cancer in a large European study (3,000+ cases, 3,000+ controls), with a per allele odds ratio of 1.3 (CI:1.12-1.49). chronic lymphocytic leukemia rs2266690 rs17028658 rs4505265 rs1045485 rs2779251 rs3136687 showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer No association seen between ...
common in clinvar
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type [OMIM:?]
common in complete genomics
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Multiple LRRK2 variants modulate risk of Parkinson disease: a Chinese multicenter study. [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2]
normal risk for gallstones
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rs11887534, a SNP in the hepatic cholesterol transporter ABCG8 gene, has been implicated in gallstone disease, a process known formally as cholelithiasis. The common allele, rs11887534(G), encodes the aspartic acid (D), while the minor (C) allele encodes histidine (H). In a study of ~1,000 German patients, the overall odds ratio associated with rs11887534(C) carriers was 2.2 (CI: 1.8-2.6, p=1.4x10<sup>-14</sup>), and for (C;C) homozygotes, 7x. Up to 10% of the population attributable risk for gallstones may be accounted for by this SNP. [PharmGKB:Curated GWAS Results: A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease (Initial Sample Size: 280 cases, 360 controls; Replication Sample Size: 2...
common on affy axiom data appears to be common on the 23andMe platform
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Rs3135506 (also known as S19W) is associated with severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls. It is discussed in ; however, the SNP that prevents weight gain from high fat diets is rs662799. [PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides and apolipoprotein B. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): triglycerides: p = 5.5 x 10(-12); ApoB: p = 8.4 x 10(-8). Type of association: CO; GN] [OMIM:?]
common in clinvar
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age related macular degeneration [OMIM:COMPLEMENT FACTOR B; CFB]
normal
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age related macular degeneration Genetic markers and biomarkers for age-related macular degeneration. C2 and CFB genes in age-related maculopathy and joint action with CFH and LOC387715 genes. Analysis of rare variants in the complement component 2 (C2) and factor B (BF) genes refine association for age-related macular degeneration (AMD). Variations in five genes and the severity of age-related macular degeneration: results from the Muenster aging and retina study. Multilocus analysis of age-related macular degeneration. Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes. Complement component 3: an assessment of association with AMD and analysis of gene-gene and gene-environment interactions in a Northern Irish...
common in complete genomics
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rs17580, also known as the S allele, is a SNP in the SERPINA1 gene. Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. See rs28929474 for the most common pathologic SNP in the SERPINA1 gene. finds no association between rs17580 and pulmonary emphysema a relatively small study of 182 patients found no association between rs17580 and risk for cholangiocarcinoma Alpha-1 Antitrypsin Deficiency [OMIM:PI S]
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
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rs7775 (R324G) osteoarthritis at multiple joints (p = 0.07), particularly in the hip in women associated with osteoarthritis of the hip in females This is an arg324-to-gly (R324G) substitution Meta-analysis of 14 studies did not support a significant association between rs7775 and osteoarthritis. Functional variants within the secreted frizzled-related protein 3 gene are associated with hip osteoarthritis in females. Genetic variation in candidate osteoporosis genes, bone mineral density, and fracture risk: the study of osteoporotic fractures. No association of the polymorphisms of the frizzled-related protein gene with peak bone mineral density in Chinese nuclear families. Variant alleles of the Wnt antagonist FRZB are determinants of hip shape and modify the relationship between hip shap...
common in clinvar appears to be common on the 23andMe platform
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[OMIM:VARIEGATE PORPHYRIA, HOMOZYGOUS]
common in clinvar
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Profound biotinidase deficiency in two asymptomatic adults. Partial biotinidase deficiency is usually due to the D444H mutation in the biotinidase gene. Mutations causing profound biotinidase deficiency in children ascertained by newborn screening in the United States occur at different frequencies than in symptomatic children. [OMIM:?]
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
ABH blood group %22Secretor%22 status if Japanese
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rs1047781, also known as Ile129Phe, is found on chromosome 19 in the alpha(1,2)-fucosyltransferase FUT2 gene. The wild-type rs1047781(A) encodes the 'Secretor' allele, while rs1047781(T) encodes the 'nonsecretor' (se2 or sej) allele. This basis for FUT2 nonsecretor status is found primarily in Japanese. In Caucasians, nonsecretor status is associated with the se1 allele of rs601338, and rs1047781 genotype shows almost no variation. In Japanese, the se1 allele is absent, but 15% of individuals are non-secretors based on being homozygous for rs1047781(T;T). [OMIM:?] [GWAS:None]
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
common in complete genomics appears common on the 23andMe microarray
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[OMIM:GAUCHER DISEASE, TYPE IIIC]
common in clinvar
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rs16022, also known as E918D, is a SNP in the calcium channel, voltage-dependent, P/Q type, alpha 1A subunit CACNA1A gene. On it's own it is not associated with migraines; however, individuals with both this SNP and a variant rs16023 have a 2x increased risk of any type of migraine, at least if a study of ~100 Italian patients is correct.
normal
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
common on affy axiom data
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rs1800054, also known as S49C, is a SNP in the ATM gene. A large meta-analysis published in 2011, comprising 26,000+ breast cancer cases and almost 30,000 controls from 23 studies in the Breast Cancer Association Consortium, found average odds ratios of 1.05 for heterozygotes and 1.51 for homozygotes of each of 5 ATM gene SNPs, of which this is one. A common coding variant in CASP8 is associated with breast cancer risk. Two-stage case-control study of common ATM gene variants in relation to breast cancer risk. Single-nucleotide polymorphisms in the p53 signaling pathway. Gene-environment interactions in 7610 women with breast cancer: prospective evidence from the Million Women Study. [OMIM:?]
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
common This appears to be the common allele among an ambiguous flip
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rs1800471 encodes a change at codon 25 of the TGFB1 gene. It is reported to predispose several organs to fibrosis, and in relation to Crohn's disease, it was associated with stricturing Crohn's disease (odds ratio 2.63, CI: 1.16-5.88, p=0.01) and a shorter time to intestinal resection (p = 0.06) in a study of several hundred Australian patients. [PharmGKB:Curated In conjunction with polymorphism at codon 10, this SNP defines high-, medium- or low-producer haplotype. The Arg allele is associated with higher blood pressure. The C allele is associated with susceptibility to EBV-associated post-transplant lymphoproliferative disorder. The C allele is associated with susceptibility to chronic periodontitis; The G allele may be associated with brucellosis susceptibility. This SNP may play a rol...
common in clinvar
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rs1800546 is located on chromosome 9q31.1 within the aldolase B fructose bisphosphate gene. rs1800546 is linked to approximately 65% of hereditary fructose intolerance (HFI) cases in those of European ancestry. The incidence of HFI in those of European ancestry is estimated to be 1 in 20,000 births. HFI is an autosomal recessive condition. The ancestral allele is C, while the risk-associated allele is G. Aldolase B is a critical enzyme involved in the breakdown of the sugar fructose through the glycolysis pathway. The C to G change results in an amino acid substitution at position 149 from alanine to proline (A149P). ==CLINICAL OVERVIEW:== Aldolase B fructose bisphosphate catalyzes the reversible reaction of fructose-1-phosphate to glyceraldehyde and dihydroxyacetone-phosphate. Further con...
common in complete genomics
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Albumin Rugby Park: a truncated albumin variant caused by a G-->C splice-site mutation in intron 13. Effect of genetic variation on the fatty acid-binding properties of human serum albumin and proalbumin. [OMIM:?]
common in complete genomics common for Caucasians on the 23andme platform
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also known as rs28933380 related to colorectal cancer, FAMILIAL, Ashkenazi * APC l1307K: Introduction - Johns Hopkins Hereditary Colorectal Cancer Website [OMIM:?]
common in complete genomics appears to be common on the 23andMe platform
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rs2066845 is a SNP in the NOD2 gene; this SNP is also known as G908R, with the (G) allele encoding the Gly (G) and the (C) allele encoding the Arg (R). rs2066845, a SNP in the NOD2 gene, has been linked to Crohn's disease. rs2066845 has also been reported, with an odds ratio of 3.5 (CI 1.51–7.01), to be associated with psoriatic arthritis. No association was found for NOD2/CARD15 SNPs (R702W, G908R) in Chinese patients with inflammatory bowel disease. [OMIM:CROHN DISEASE, SUSCEPTIBILITY TO]
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0010 [OMIM:?]
common in clinvar appears common on the 23andMe microarray
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[OMIM:CARDIOMYOPATHY, DILATED, 1A]
common in clinvar appears common on the 23andMe microarray
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[OMIM:WERNER SYNDROME, ATYPICAL]
common in clinvar appears common on the 23andMe microarray
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[OMIM:ACROMESOMELIC DYSPLASIA, MAROTEAUX TYPE]
common in complete genomics appears common on the 23andMe microarray
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Modifier effects between regulatory and protein-coding variation. [OMIM:EPISODIC ATAXIA, TYPE 1]
common in clinvar appears common on the 23andMe microarray
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[OMIM:RETINITIS PIGMENTOSA 4]
common in clinvar appears common on the 23andMe microarray
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[OMIM:RETINITIS PIGMENTOSA 4]
common in clinvar
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[OMIM:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, MONTREAL TYPE]
common in clinvar
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[OMIM:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, GARY TYPE]
common in clinvar appears common on the 23andMe microarray
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[OMIM:CONE-ROD DYSTROPHY 6]
common in clinvar appears common on the 23andMe microarray
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[OMIM:TOOTH AGENESIS, SELECTIVE, 3]
common in clinvar appears common on the 23andMe microarray
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[OMIM:CLEFT PALATE WITH ANKYLOGLOSSIA]
common in clinvar appears common on the 23andMe microarray
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[OMIM:THYROID CARCINOMA WITH THYROTOXICOSIS]
common in clinvar
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This snp has now been studied extensively. full text available from plos [OMIM:AMYLOIDOSIS, CEREBROARTERIAL, ICELANDIC TYPE]
common in clinvar
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[Single nucleotide polymorphism and haplotype in TBX1 gene of patients with conotruncal defects: analysis of 130 cases]. [OMIM:CONOTRUNCAL ANOMALY FACE SYNDROME/VELOCARDIOFACIAL SYNDROME]
common in clinvar appears common on the 23andMe microarray
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[OMIM:BEST MACULAR DYSTROPHY]
common in clinvar appears common on the 23andMe microarray
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[OMIM:ERYTHROCYTOSIS, FAMILIAL, 2]
common in clinvar appears common on the 23andMe microarray
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[OMIM:CEROID LIPOFUSCINOSIS, NEURONAL, 8]
common in clinvar For 23andMe users, this is the normal genotype. However see also Rs28940871(G;G)
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This position appears to have been flipped between b36 and b37. Extra scrutiny is warranted. rs28940871, also known as Leu451Val, L451V, or C1351G, is a mutation in the HEXA gene. Some variations of this gene are associated with Tay-Sachs disease. In a population of Iraqi Jews, this SNP was found in 21 of 62 Tay-Sachs disease carriers (33.9%) and in 0 of 100 noncarriers. The authors estimated that this SNP originated sometime between 1519 BC and 635 AD, with 442 BC as the best estimate (+/- 1,000 years). The Iraqi Jewish community started around 586 BC when the Babylonian king Nebuchadnezzar deported 10,000 to 40,000 of the Jews from the kingdom of Judea to Babylon. This was probably the time of separation of the Iraqi Jews from the rest of the Jewish people. OMIM 23andMe reports the risk ...
common in clinvar appears common on the 23andMe microarray
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[OMIM:BEST MACULAR DYSTROPHY]
common in clinvar appears to be common on the 23andMe platform
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[OMIM:MOSAIC VARIEGATED ANEUPLOIDY SYNDROME]
common in complete genomics
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Researchers suggest that BARD1 Cys557Ser (rs28997576) is an ancient variant that confers risk of single and multiple primary breast cancers, and this risk is amplified in carriers of the BRCA2 999del5 (codon 257, exon 9) mutation. [OMIM:BREAST CANCER, SUSCEPTIBILITY TO]
common in clinvar
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Hb Monroe or alpha 2 beta 230(B12)Arg----Thr, a variant associated with beta-thalassemia due to A G----C substitution adjacent to the donor splice site of the first intron. Beta thalassemia due to a novel mutation in IVS 1 sequence donor site consensus sequence creating a restriction site. Expression of a beta thalassemia gene with abnormal splicing. Beta-thalassaemia in Cubans: novel allele increases the genetic diversity at the HBB locus in the Caribbean. Intrinsic differences between authentic and cryptic 5' splice sites. ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of beta-thalassaemia. A new mutation in IVS-1 of the human beta globin gene causing beta thalassemia due to abnormal splicing. The molecular basis of beta thalassaemia i...
normal
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Also known as R1628P, rs33949390 is a SNP in the LRRK2 gene. A study of Chinese patients with Parkinson's disease concluded that in this population, after adjustments were made for age, age of onset, and gender, rs33949390(C) carriers were 3.3x more likely to develop the disease than noncarriers (CI: 1.4- 7.9, p = 0.007). [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2]
common in clinvar
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A new mutation at IVS1 nt 2(T----A), in beta-thalassemia from Algeria. Severe Hb S-beta zero-thalassaemia with a T----C substitution in the donor splice site of the first intron of the beta-globin gene. An African origin for an 'American black' beta zero-thalassemia mutation? Intrinsic differences between authentic and cryptic 5' splice sites. Real-time PCR for single-cell genotyping in sickle cell and thalassemia syndromes as a rapid, accurate, reliable, and widely applicable protocol for preimplantation genetic diagnosis. Mutation analysis of the HBB gene in selected Bangladeshi beta-thalassemic individuals: presence of rare mutations. [OMIM:?]
common in complete genomics
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beta 0 thalassemia, a nonsense mutation in man. Human gene mutation database-a biomedical information and research resource. [OMIM:?]
common in clinvar
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Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/ The beta-thalassaemia mutations in the population of Cyprus. Novel promoter and splice junction defects add to the genetic, clinical or geographic heterogeneity of beta-thalassaemia in the Portuguese population. Molecular basis of beta-thalassemia in Turkey: detection of rare mutations by direct sequencing. The peculiar spectrum of beta-thalassemia genes in Tunisia. beta-Thalassemia in American Blacks: novel mutations in the 'TATA' box and an acceptor splice site. Significance of borderline hemoglobin A2 values in an Italian population with a high prevalence of beta-thalassemia.
common in clinvar
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Phenotype characterization and DSPP mutational analysis of three Brazilian dentinogenesis imperfecta type II families.
common in clinvar
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The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. 23andMe tests for SNPs in the MEFV gene that are associated with a recessive form of familial Mediterranean fever: * rs28940579, also known as V726A (risk allele G) * rs28940580, also known as M680I C>G (risk allele G) * rs28940578, also known as M694I (risk allele T) * rs3743930, also known as E148Q (risk allele G) * rs11466023, also known as P369S (risk allele A) * i4000406, also known as M694V (risk allele C) * i4000409, also known as A744S (risk allele A) * i4000403, also known as F479L (risk allele C) * i4000410, also known as R761H (risk allele T) * i40...
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0005 [OMIM:?]
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0008 [OMIM:?]
common in clinvar
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Presenile dementia and cerebral haemorrhage linked to a mutation at codon 692 of the beta-amyloid precursor protein gene. Presenile Alzheimer dementia characterized by amyloid angiopathy and large amyloid core type senile plaques in the APP 692Ala-->Gly mutation. Flemish and Dutch mutations in amyloid beta precursor protein have different effects on amyloid beta secretion. Presentation of amyloidosis in carriers of the codon 692 mutation in the amyloid precursor protein gene (APP692). In vitro studies of amyloid beta-protein fibril assembly and toxicity provide clues to the aetiology of Flemish variant (Ala692-->Gly) Alzheimer's disease. [OMIM:?]
common in clinvar
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Characterization of chicken liver dihydrofolate reductase after purification by affinity chromatography and isoelectric focusing. Single-amplicon MSH2 A636P mutation testing in Ashkenazi Jewish patients with colorectal cancer: role in presurgical management. Homozygosity of MSH2 c.1906G-->C germline mutation is associated with childhood colon cancer, astrocytoma and signs of Neurofibromatosis type I. Classifying MLH1 and MSH2 variants using bioinformatic prediction, splicing assays, segregation, and tumor characteristics. The rate of the predominant Jewish mutations in the BRCA1, BRCA2, MSH2 and MSH6 genes in unselected Jewish endometrial cancer patients. High risk of colorectal and endometrial cancer in Ashkenazi families with the MSH2 A636P founder mutation. [OMIM:?]
common in clinvar
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Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays. [OMIM:?]
2081 snps
(hide) Coffee
can taste bitter
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rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you. (G;G)...
Magnitude: 0.1
Frequency: 47.8%
References:6
Frequency: 47.8%
References:6
can taste bitter
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rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
can taste bitter
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
normal
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
common on affy axiom data
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rs2472297 is a SNP located between the CYP1A1 and CYP1A2 genes on ch 15q24. A meta-analysis of four GWAS studies of coffee consumption among a total of ~8,000 coffee drinkers of European ancestry found that the rs2472297(T) was strongly associated with increased consumption (p = 5.4 x 10e-14). The estimated effect was an increase of 0.2 cups a day per allele for both this SNP and one other (rs6968865).
5 snps
(hide) Coriell Personalized Medicine Collaborative
1.3x risk of prostate cancer 1.4x risk of prostate cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neighbor, rs1447295. The odds ratio for heterozygotes is estimated to be 1.26 (CI: 1.13 - 1.41)...
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
1.3x higher risk of ER+ breast cancer
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rs2981582 in the FGFR2 gene was one of the four strongest associations found in a genome-wide association study (GWAS) of over 4,000 breast cancer samples. The T allele was more strongly related to ER-positive (per-allele odds ratio 1.31 (CI: 1.27-1.36)) than ER-negative (odds ratio 1.08 (CI:1.03-1.14)) disease (p for heterogeneity = 10(-13)). While on its own still of fairly small effect, this was the most significant of 7 SNPs to help estimate risk of breast cancer. Family history and/or BRCA1 or BRCA2 testing status are more significant factors, which were not part of this panel. Based on a study of 1,049 Chinese breast cancer patients, carriers of risk alleles at three SNPs (rs2981582, rs1219648 and rs2420946) were at 1.36x increased risk for breast cancer (CI: 1.13-1.62, p = 0.001). A...
1.3x increased risk for type-2 diabetes
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
1.5x increased risk for CAD 1.5x higher risk for coronary artery disease
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rs1333049 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is most likely (C); the odds ratio associated with heterozygotes is 1.47 (CI 1.27-1.70), and for homozygotes, 1.9 (CI 1.61-2.24). This SNP has also been reported to have the highest association of any SNP studied in a subsequent experiment conducted with the resources of the German MI [Myocardial Infarction] Family Study. The initial studies were conducted on Caucasian populations. A subsequent study of Japanese and Korean patients has also found rs1333049 to be associated with increased coronary artery disease risk, with roughly similar odds ratios. A long-term study of a cohort of 769 individuals finds that the rs1333049(C...
Magnitude: 2
Frequency: 43.1%
References:10
Frequency: 43.1%
References:10
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
complex; see details
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rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...
None
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*3, defined as the common loss of function variant rs1057910(C) (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/. Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of nonsteroidal anti-inflammatory drugs (NSAIDs) that are CYP2C8 or CYP2C9 substrates, such as aceclofena...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
Magnitude: 0.1
Frequency: 91.8%
Repute:Bad
References:88
Frequency: 91.8%
Repute:Bad
References:88
normal, but higher risk for certain autoimmune diseases
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
normal
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rs9272346 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 5.49 (CI 4.83-6.24), and for homozygotes, 18.52 (CI 12.69-27.03). Note that the (A) allele is the most common in various human populations; instead of labeling (A) as a risk allele, we could consider the (G) allele protective. Risk alleles for multiple sclerosis identified by a genomewide study. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. [PharmGKB:Curated GWAS ...
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
Magnitude: 0
Frequency: 61.1%
Repute:Good
References:44
Frequency: 61.1%
Repute:Good
References:44
normal
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rs10490924 was identified as a risk factor from chromosome 10 related to age related macular degeneration. The risk allele is (T). Odds ratios for heterozygotes and homozygotes are, respectively, 2.69 (CI: 2.22-3.27) and 8.21 (CI: 5.79-11.65). Disease risk in combination with the rs1061170 SNP in the CFH gene is dramatically increased. Homozygotes for both the rare/risk alleles at both loci are estimated to be at 57 fold higher risk for age related macular degeneration than individuals homozygous for the common alleles at both loci. A subsequent study indicated that the risk based on solely the ARMS2 SNP rs10490924 is significantly higher in smokers than in non-smokers. Based on a study of ~750 patients, rs10490924 is significantly higher in participants with choroidal neovascularization t...
normal
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CPMC uses this to indicate increased risk of Systemic lupus erythematosus. [GWAS:Systemic lupus erythematosus]
normal
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rs6920220 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.20 (CI 1.06-1.36), and for homozygotes, 1.72 (CI 1.33-2.22). rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allele of rs13207033 was strongly associated with RA when compared to carriage of none [OR of 1.86 (95% CI) (1.51-2.29)]. This equates to an effect size of 1.50 (95% CI 1.21-1.85) Lack of association or interactions between the IL-4, IL-4Ralpha an...
normal
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2,019 cases and 2,105 controls. Using pooling, we identified a new melanoma risk locus on chromosome 20 (rs910873 and rs1885120 combined P less than 1 10-15. The per allele odds ratio was 1.75 (1.53, 2.01), with evidence for stronger association in early-onset cases. [PharmGKB:Curated GWAS Results: Common sequence variants on 20q11.22 confer melanoma susceptibility (Initial Sample Size: 864 cases, 864 controls; Replication Sample Size: 1,230 cases, 1,251 controls; Risk Allele: rs910873-T). This variant is associated with Melanoma.] [OMIM:MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 7; CMM7] [GWAS:Melanoma]
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who actually develop...
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:48
Frequency: 93.8%
Repute:Good
References:48
normal risk
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rs16901979 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In some studies, the regions have been divided, and this SNP falls in region 2. In a study of over 3,600 Caucasians with prostate cancer, rs16901979 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs16901979(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.53 (CI: 1.22-1.92, p=1.8x10e-4) and may account for 3.6% of population attributable risk. cancer related according to this blog Two genetic markers in the 8q24 region of chromosome 8 rs7008482 and rs16901979 have been linked to an increased risk of prostate cancer in African Americans. abstract In follow-up studies looki...
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
normal
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The rs72558186(A) SNP represents a CYP2C19 allele known as CYP2C19*7; it reflects a splice donor mutation that leads to a poor metabolizer phenotype. This SNP is also known as CYP2C19_19294T>A, and in the Affymetrix DMET panel, as DMET3B10072. Note: absence of allele frequency data leaves this as a possible ambiguous flip.
30 snps
(hide) CYP1A2
Magnitude: 2
Your CYP1A2 fast metabolizer status means that you are less stimulated by caffeine. Ciprofloxacin is also metabolized by CYP1A2, but is unclear if your genotype should influence its effect.
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[GWAS:None]
CYP1A2_1545T>C homozygote
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rs2470890 is a SNP in the CYP1A2 gene. The rs2470890(C) allele defines the CYP1A2_1545T>C variant. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [PharmGKB:Curated Weakly associated with tardive dyskinesia and schizophrenia.]
References:1
also known as F186L, Phe186Leu, c.558C>A, g.32755C>A, g.45833194C>A According to the literature, this is the cause of the CYP1A2*11 homozygote which produces 5% Vmax of the normal enzyme level. However 23andMe data shows that A is more common. in allele CYP1A2*11; drastic reduction in O-deethylation of phenacetin and 7-ethoxyresorufin; has a Vmax of approximately 5% of that of the wild-type and 5-fold lower Km value.
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rs72547513, also known as 558C>A or F186L, is a SNP in the CYP1A2 gene. 23andMe and opensnp show A as more common. dbSNP shows C as the reference, and A as the variant, but doesn't have any population frequency information. claims that A is the variant, and that it defined the CYP1A2*11 allele with a Vmax approximately 5% of that of the CYP1A2 wild type, and reduced enzymatic activity.
normal
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
common on affy axiom data
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rs2472297 is a SNP located between the CYP1A1 and CYP1A2 genes on ch 15q24. A meta-analysis of four GWAS studies of coffee consumption among a total of ~8,000 coffee drinkers of European ancestry found that the rs2472297(T) was strongly associated with increased consumption (p = 5.4 x 10e-14). The estimated effect was an increase of 0.2 cups a day per allele for both this SNP and one other (rs6968865).
normal
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rs2069526 is a SNP in the CYP1A2 gene. The rs2069526(T) allele defines the CYP1A2*1K_-739T>G variant. [PharmGKB:Curated Present in reduced function haplotype, unlikely to be causative.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
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rs12720461 is a SNP in the CYP1A2 gene. The rs12720461(T) allele defines the CYP1A2*1K_-729C>T variant. [PharmGKB:Curated Likely disrupts transcription factor binding, leading to reduced function.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28399424, also known as 5090C>T or R431W, is a SNP in the CYP1A2 gene. The rs28399424(T) allele defines the CYP1A2*6 decreased activity variant. [PharmGKB:Curated Reduced expression.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs55889066, also known as 3497G>A or C406Y, is a SNP in the CYP1A2 gene. The rs55889066(A) allele defines the CYP1A2*5 variant. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: In an in vitro system, this variant showed no catalytic activity against the carcinogen NNK. The wild type protein bioactivates this carcinogen. The variant also produced extra metabolites of phenacetin that were not observed with the wild type protein. Type of association: FA]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs56276455, also known as 2385G>A, 5347T>C or D348N is a SNP in the CYP1A2 gene. The rs56276455(A) allele defines the CYP1A2*3 variant.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs72547515, also known as 2473G>A, 5347T>C or R377Q, is a SNP in the CYP1A2 gene. The rs72547515(T) allele defines the CYP1A2*16 variant.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs72547517, also known as 5166G>A, 5347T>C or R456H, is a SNP in the CYP1A2 gene. The rs72547517(A) allele defines the CYP1A2*8 variant. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: In an in vitro system, this variant showed no activity for the drug substrates clozapine or phenacetin even at the highest substrate and double membrane concentrations, it also showed reduced expression of holoprotein in bacterial cells. Type of association: FA]
normal
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rs72547516, also known as 2499A>T or I386F, is a SNP in the CYP1A2 gene. The rs72547516(T) allele defines the CYP1A2*4 variant. [PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: In an in vitro system, this variant showed no activity for the drug substrates clozapine or phenacetin even at the highest substrate and double membrane concentrations, it also showed reduced expression of holoprotein in bacterial cells. Type of association: FA]
1 genoset 13 snps
(hide) CYP2A6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[PharmGKB:In-Depth This variant results in a truncated protein and no enzyme activity; part of the CYP2A6*20 haplotype.]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
common in complete genomics
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CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. [PharmGKB:In-Depth This variant decreases enzyme activity and affects metabolism of coumarin and nicotine; part of the CYP2A6*17 haplotype.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the *10 haplotype and affects nicotine metabolism.]
common in complete genomics
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[PharmGKB:In-Depth This variant affects heat stability and affects nicotine metabolism; part of the CYP2A6*7 and CYP2A6*10 haplotypes.]
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
5 snps
(hide) CYP2C19
Magnitude: 3
CYP2C19 Intermediate Metabolizer. Your body breaks down some medicines at a slightly slower than normal rate (which is represented by gs150). Individuals with gs152 genotypes have even slower metabolism. *anti-epileptics (such as diazepam, phenytoin, and phenobarbitone) *anti-depressants (such as amitriptyline and clomipramine) *anti-platelet drug clopidogrel (Plavix) *anti-ulcer proton pump inhibitors like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid) *hormones (estrogen, progesterone).
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 2
Frequency: 43.1%
References:10
Frequency: 43.1%
References:10
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
Frequency: 22.7%
References:1
References:1
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[GWAS:Acenocoumarol maintenance dosage]
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Association of warfarin dose with genes involved in its action and metabolism. The largest prospective warfarin-treated cohort supports genetic forecasting.
References:0
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The rs72558185(G) SNP is an insertion variant in the CYP2C19 gene; it is also known as hCV34328665, and is in the Affymetrix DMET panel.
normal
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The rs5787121(-) (i.e. deletion) SNP defines the CYP2C19 allele known as G439- or 90052delG.
normal
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The rs3758581(A) SNP defines a CYP2C19 allele known as V331I. Analysis of 50 SNPs in CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOF mass spectrometry in Chinese Han population.
normal
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The rs6413438(T) allele defines the CYP2C19 allele known as CYP2C19*10. This allele may lead to reduced metabolism of S-mephenytoin at least in vitro. [PharmGKB:Curated This variant is the defining SNP for CYP2C19*10. This variant is associated with reduction in the metabolism of S-mephenytoin in vitro.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17882687(C) SNP defines the CYP2C19 allele known as CYP2C19*15, and also known as CYP2C19_55A>C or I19L.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17884712(A) allele defines the CYP2C19 variant known as CYP2C19*9, which is associated with a slight decrease in the metabolism of S-mephenytoin (at least in vitro). [PharmGKB:Curated This variant is the defining SNP for CYP2C19*9 and associated with a modest decrease in the V(max) for 4'-hydroxylation of S-mephenytoin in vitro.]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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The rs55752064(C) SNP defines the CYP2C19 allele known as CYP2C19*14, also known as L17P.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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The rs72552267(A) SNP defines the CYP2C19 allele known as CYP2C19*6, also known as R132Q.
normal
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
normal
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The rs72558186(A) SNP represents a CYP2C19 allele known as CYP2C19*7; it reflects a splice donor mutation that leads to a poor metabolizer phenotype. This SNP is also known as CYP2C19_19294T>A, and in the Affymetrix DMET panel, as DMET3B10072. Note: absence of allele frequency data leaves this as a possible ambiguous flip.
1 genoset 20 snps
(hide) CYP2C9
warfarin sensitivity (~2.5 mg/day)
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rs8050894, is located on chromosome 16 in the gene VKORC1. VKORC1 is the primary target of the drug warfarin (Coumadin), a commonly used oral anticoagulant. rs8050894 is one of several polymorphisms found in VKORC1 that is associated with specific warfarin doses (). Other polymorphisms in VKORC1 (rs7196161, rs9923231, rs9934438, rs2359612) are equally predictive of warfarin dose requirement in both European and Asian-descent individuals. Other polymorphisms found in the gene cytochrome P450 2C9 (CYP2C9) influence the metabolism of warfarin and have a smaller effect on warfarin dose. These polymorphisms are rs1799853 (CYP2C9*2) and rs1057910 (CYP2C9*3). In several hundred Europeans, no association was found between rs8050894 and risk for ischemic stroke. Genetic-based dosing in orthopedic p...
CYP2C9 extensive metabolizers. This is normal.
Frequency: 27.4%
References:2
References:2
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[Distribution of variant alleles association with warfarin pharmacokinetics and pharmacodynamics in the Han population in China].
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[PharmGKB:Curated In a GWAS study, this SNP was modestly associated with warfarin dose, and was in perfect linkage disequilibrium with rs4086116.]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*3, defined as the common loss of function variant rs1057910(C) (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/. Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of nonsteroidal anti-inflammatory drugs (NSAIDs) that are CYP2C8 or CYP2C9 substrates, such as aceclofena...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
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A genome-wide association study of acenocoumarol maintenance dosage. [PharmGKB:Curated In a GWAS study, this SNP was modestly associated with warfarin dose, accounting for ~9% of the variance in dose. This SNP was in perfect linkage disequilibrium with rs4917639.] [GWAS:Warfarin maintenance dose]
Magnitude: 0
Frequency: 86.6%
Repute:Good
References:3
Frequency: 86.6%
Repute:Good
References:3
normal
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rs9332130, also known as 815A>G, 10598A>G or E272G, is a SNP in the CYP2C9 gene. The rs9332130(G) allele defines the CYP2C9*10 variant.
normal
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rs2256871, also known as 752A>G, 10535A>G or H251R, is a SNP in the CYP2C9 gene. The rs2256871(C) allele defines the CYP2C9*9 variant.
normal
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rs1057909 is a SNP in the CYP2C9 gene. The rs1057909(G) allele defines the CYP2C9_42612A>G variant, about which little is known.
normal
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rs9332239, also known as 1465C>T, 50338C>T or P489S, is a SNP in the CYP2C9 gene. The rs9332239(T) allele defines the CYP2C9*12 variant. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504.
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs72558190, also known as 485C>A or S162X, is a SNP in the CYP2C9 gene. The rs72558190(A) allele defines the CYP2C9*15 variant, which is inactive.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs7900194, also known as 449G>A, 3627G>A or R150H, is a SNP in the CYP2C9 gene. The rs7900194(A) allele defines the CYP2C9*8 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a mod...
normal
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rs1057911 is a SNP in the CYP2C9 gene. The rs1057911(T) allele defines the CYP2C9_50298A>T variant, about which little is known. Warfarin
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
1 genoset 20 snps
(hide) CYP2D6
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 2
CYP2D6*41 decreased metabolism
Homozygous for CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
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a variation in CYP2D6
References:0
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a variation in CYP2D6
References:0
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a variation in CYP2D6
References:1
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[PharmGKB:In-Depth Causes deletion of amino acid, K281. Contrary to in vitro results, in vivo study has cast doubt on whether or not this variant leads to reduced function.]
References:0
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a variation in CYP2D6
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a variation in CYP2D6
References:5
carrier of one CYP2D6*41 allele
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
References:0
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a variation in CYP2D6
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a variation in CYP2D6
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
normal normal
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rs5030656, also known as 2615_2617delAAG or K281del, is a SNP in the CYP2D6 gene. The rs5030656(-) allele defines the CYP2D6*9 variant, which has decreased activity.
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
normal
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Also known as 1858C>T, the (A) allele is a marker for CYP2D6*4F non-functioning variant.
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a variation in CYP2D6
normal
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2938C>T marker. The (A) allele indicates non-functioning CYP2D6*4G variant.
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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1973_1974insG insertion is a marker for the CYP2D6*20 non-functioning variant.
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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a variation in CYP2D6
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs28371706, also known as 1023C>T or T107I, is a SNP in the CYP2D6 gene. The rs28371706(T) allele is found in several CYP2D6 variants: * CYP2D6*17 decreased activity variant * CYP2D6*40 non-functioning variant * CYP2D6*58 variant * CYP2D6*64 variant [PharmGKB:In-Depth Variant was identified as being part of the reduced function haplotype CYP2D6*17.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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a variation in CYP2D6
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs5030867, also known as 2935A>C or H324P, is a SNP in the CYP2D6 gene. The rs5030867(C) allele defines the CYP2D6*7 variant, which is inactive.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the reduced functioning haplotype CYP2D6*29, which is found at an estimated allele frequency of 20% in African Tanzanians.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common on affy axiom data
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[PharmGKB:In-Depth This variant is part of the reduced functioning haplotype CYP2D6*29, which is found at an estimated allele frequency of 20% in African Tanzanians.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
1 genoset 85 snps
(hide) CYP2E1
normal
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rs2515641 is a SNP in the CYP2E1 gene. The rs2515641(T) allele defines the CYP2E1_10463T>C(F421F) variant.
normal
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rs6413420 is a SNP in the CYP2E1 gene. The rs6413420(T) allele defines the CYP2E1*7_-71G>T variant.
normal
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rs2031920 is a SNP in the CYP2E1 gene. The rs2031920(T) allele defines the CYP2E1_-1055C>T variant. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
normal
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rs2070672 is a SNP in the CYP2E1 gene. The rs2070672(G) allele defines the CYP2E1*7_-352A>G variant.
normal
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rs4646976 is a SNP in the CYP2E1 gene. The rs4646976(G) allele defines the CYP2E1_marker8 variant, as used in the 2008 study determining the 16 most common CYP2E1 haplotypes world-wide.(see CYP2E1 for details)
normal
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rs6413419, also known as 4768G>A or V179I, is a SNP in the CYP2E1 gene. The rs6413419(A) allele defines the CYP2E1*4 variant.
normal
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rs915909 is a SNP in the CYP2E1 gene. The rs915909(T) allele defines the CYP2E1_6498C>T(I321I) variant.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs55897648, also known as 10023G>A or V389I, is a SNP in the CYP2E1 gene. The rs55897648(A) allele defines the CYP2E1*3 variant.
normal
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rs2070673 is a SNP in the CYP2E1 gene. The rs2070673(A) allele defines the CYP2E1*7_-333T>A variant.
normal
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rs2070676, also known as 9896C>G, is a SNP in the CYP2E1 gene. The rs2070676(G) allele defines the CYP2E1*1B variant.
normal
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Also known as CYP2E1_-1295G>C, this SNP is reported to mark the c2 allele of CYP2E1. The rs3813867(C) allele defines the CYP2E1_-1295G>C variant allele. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
18 snps
(hide) CYP3A5
You appear to be a CYP3A5 expressor. This is normal. However it is still possible you carry variations which were not tested by your platform.
normal
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rs1057868, also known as A503V, is a relatively common variant defining the POR*28 allele of the P450 (cytochrome) oxidoreductase POR gene. The POR gene encodes a protein involved in electron transport of cytochrome p450 enzymes such as CYP3A4, CYP3A5 and CYP3A7. A study of 251 individuals from two independent studies (182 patients treated with methadone and 69 patients with clozapine) for CYP3A activity found that CYP3A SNPs themselves did not predict particularly well inter-individual variability in overall CYP3A activity. However, rs1057868(T;T) individuals had a 1.6x increased CYP3A activity compared to rs1057868(C) carriers (n=182, p=0.004), and the finding was replicated in a second independent dataset. The authors conclude that this POR gene SNP is a better predictor of overall CYP3...
References:1
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rs41303343, also known as 27131_27132insT, is a SNP in the CYP3A5 gene. The rs41303343(T) allele defines the CYP3A5*7 variant, which is nonfunctional.
common in complete genomics
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rs776746, also known as 6986G>A, is a SNP encoding the (nonfunctional) CYP3A5*3 allele of the CYP3A5 gene. CYP3A5*3 has been studied especially in connection with the metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. The optimal therapeutic dose is in a relatively narrow window, so blood concentration monitoring is recommended. CYP3A5*3 carriers tend to build up higher levels of tacrolimus than CYP3A5*1 carriers, unless their tacrolimus intake is reduced. Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Prevalence of common dis...
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:1
Frequency: 98.2%
Repute:Good
References:1
normal
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rs28365083, also known as 27289C>A, is a SNP in the CYP3A5 gene. The rs28365083(A) allele defines the CYP3A5*2 variant, which is nonfunctional. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Genotyping panel for assessing response to cancer chemotherapy. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:7
Frequency: 100.0%
Repute:Good
References:7
normal
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rs10264272, also known as 14690G>A, is a SNP in the CYP3A5 gene. indicates that this corresponds with CYP3A5*6, however, this seems doubtful. CYP3A5 allele nomenclature found at http://www.cypalleles.ki.se/cyp3a5.htm indicates that CYP3A5*6 (also known as 14690G>A) is a splicing defect resulting in essentially no activity in the gene. This does not correspond with dbSNP, which indicates that is a nucleotide substition (624G-A) which only results in a 'silent' substitution of AAG (Lysine) to AAA (Lysine). [PharmGKB:In-Depth Nonfunctional allele present predominantly in the African American population.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs28383468, also known as 3705C>T or H30Y, is a SNP in the CYP3A5 gene. The rs28383468(T) allele defines the CYP3A5*H30Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28383479, also known as 19386G>A, is a SNP in the CYP3A5 gene. The rs28383479(A) allele defines the CYP3A5*9 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279854, also known as 29748T>C or F446S, is a SNP in the CYP3A5 gene. The rs41279854(G) allele defines the CYP3A5*10 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279857, also known as 7298C>A or S100Y, is a SNP in the CYP3A5 gene. The rs41279857(T) allele defines the CYP3A5*S100Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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should this be an A/G or a C/T? rs55817950, also known as 3699C>T, is a SNP in the CYP3A5 gene. The rs55817950(A) allele defines the CYP3A5*8 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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should this be an A/C or a G/T? rs56244447, also known as L82R, is a SNP in the CYP3A5 gene. The rs56244447(C) allele defines the CYP3A5*3D variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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should this be an A/G or a C/T? rs56411402, also known as 14665A>G or Q200R, is a SNP in the CYP3A5 gene. The rs56411402(C) allele defines the CYP3A5*4 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs72552791, also known as 3775A>G or Y53C, is a SNP in the CYP3A5 gene. The rs72552791(G) allele defines the CYP3A5*11 variant, which is nonfunctional.
1 genoset 13 snps
(hide) DCDC2
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[OMIM:?]
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[OMIM:?]
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[OMIM:?]
increased dyslexia risk
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Rs807701, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (C). One study reports that the odds ratio for rs807701 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs807701(C;C) increased from 1.88 (95% CI 0.89-3.97; P=.058) for the larger group up to 5.04 (95% CI 1.35-18.88; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs793862, the (haplotype) GRR also increased for the homozygous haplotype rs793862(A)-rs807701(C), from 4.11 (95% CI 2.77-6.08; P<.0001) for the ...
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[GWAS:None]
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Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia.
common
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Rs793862, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (A). One study reports that the odds ratio for rs793862 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs793862(A;A) increased from 3.15 (95% CI 1.30-7.66; P=.011) for the larger group up to 5.40 (95% CI 1.27-23.01; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs807701, the (haplotype) GRR also increased for the homozygous haplotype A-C, from 4.11 (95% CI 2.77-6.08; P<.0001) for the larger group, up to ...
8 snps
(hide) Doi:10.1186/1471-2156-10-88
Accelerated lung decline in smokers
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
CYP1A2_1545T>C homozygote
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rs2470890 is a SNP in the CYP1A2 gene. The rs2470890(C) allele defines the CYP1A2_1545T>C variant. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [PharmGKB:Curated Weakly associated with tardive dyskinesia and schizophrenia.]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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[OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
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Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis. [OMIM:MYELOMA, MULTIPLE]
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prostate cancer treatment response rs2279115 and rs7121 Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies. Polymorphism in maternal LRP8 gene is associated with fetal growth. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PTHR1 mutations associated with Ollier disease result in receptor loss of function. Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. A sensitive functional assay reveals frequent loss of genomic imprinting in human placenta. Association of the GNAS locus with severe malaria. Dev...
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[GWAS:Age-related macular degeneration]
Frequency: 40.7%
References:2
References:2
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[PharmGKB:Curated Variant was identified in a cohort of 54 Japanese individuals, who were administered the anti-arrhythmic drug amiodarone. (HapMap SNP)]
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[PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.0097 (ANOVA); p = 0.0013 (QMIS); p = 0.0040 (KW) Type of association: PK.]
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[GWAS:None]
Frequency: 82.3%
References:9
References:9
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rs17887200 and rs12951053 associated with ER negative breast cancer tumors (1.48 (1.11-1.93) p-trend = 0.01 and 1.29 (1.06-1.58) p-trend = 0.009, respectively) A study population including a total of 5,206 invasive ovarian cancer cases (2,829 of which were serous) and 8,790 controls found an association between rs12951053 and serous invasive cancer (median per allele odds ratio 1.19, CI: 1.01-1.38).
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A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene.
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
normal
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rs13181 is a SNP of the XPD/ERCC2 gene. A meta-analysis of 20 studies, comprising 2,308 cases, ultimately concluded that the rs13181(G) allele is associated with increased cutaneous melanoma risk (odds ratio 1.12, CI: 1.03-1.21, p = 0.01; population attributable risk = 9.6%). Polymorphisms in XPD and TP53 and mutation in human lung cancer. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. ERCC1 and ERCC2 polymorphisms and adult glioma. [Correlation of genetic polymorphisms in nucleotide excision repair system to sensitivity of advanced non-small cell lung cancer patients to platinum-based chemotherapy]. Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Risk of non-Hodgk...
normal
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
blue/gray eyes more likely
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rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page. [PharmGKB:Curated A haplotype containing rs11855019, rs6497268 and rs7495174 was highly associated with eye color, hair color and skin pigmentation in a mostly Northern European twin study.] [OMIM:OCA2 GENE]
generally non-European, but if European, 7x more likely to have black hair
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pi...
26 snps
(hide) DRD4
decreased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The G allele was associated with a decreased risk of schizophrenia.
Magnitude: 1.2
Frequency: 55.8%
References:4
Frequency: 55.8%
References:4
decreased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The C allele was associated with an decreased risk of schizophrenia. [PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
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[PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
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Association and synergistic interaction between promoter variants of the DRD4 gene in Japanese schizophrenics. [PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
6 snps
(hide) Drugbank
poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
more pain [http://blog.23andme.com/2009/08/13/snpwatch-genetic-variation-in-morphine-receptor-may-play-a-part-in-coping-with-social-rejection/] associated with needing more morphine for pain relief after surgery and heightened responses to social rejection. stronger cravings for alcohol; if alcoholic, naltrexone treatment 2x more successful
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
normal, but higher risk for several conditions ostensibly the 'normal' form, however variation is common, and each genotype seems to show some good and bad consequences.
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
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rs4675690 is in close proximity to CREB1, and adjacent to LOC151194. g2b2mh blog individuals with the TT genotype at rs4675690 (C/T) showed less disgust, but not happiness, desire or fear. T allele associated with increased chance of suicide (OR = 2.3, 95% CI 1.3-2.9, TT homozygotes vs CC homozygotes?) during the first 30 days (p > 0.05 after the first month) of citalopram treatment, in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males...
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
faster responder
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This SNP in the ACE gene, also known as G12269A, is reported to influence how quickly African Americans respond to the anti-hypertensive drug ramipril. rs4344(A;A) and rs4344(G;G) homozygotes are able to reach lower blood pressure levels upon treatment with ramipril sooner than rs4344(A;G) heterozygotes. The odds ratio reported for this study, comparing both homozygotes to heterozygotes, is 1.86 (CI: 1.32-3.23). Note that this SNP is in almost complete linkage disequilibrium with the insertion/deletion ACE gene SNP.
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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[PharmGKB:Curated This SNP on chromosome 1 was associated with the susceptibility to daunorubicin-induced cytotoxicity in the YRI population using International HapMap cell lines.]
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: A-444C was associated with aspirin-induced urticaria (AIU). The C allele was more frequent in patients with the cutaneous pattern of AIU and in patients with low skin reactivity to histamine. Study size: 110 patients with AIU and 165 nonallergic controls .]
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[PharmGKB:Curated This SNP at chromosome 9 is significantly associated with HNRPD expression (located on chromosome 4), and daunorubicin IC50 in CEU population using International HapMap cell lines.]
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[PharmGKB:Curated This variant is in intron 4 of PICK1 and has been significantly associated with methamphetamine abusers with spontaneous relapse of psychosis.]
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rs20455, often called Arg719 or 719Arg, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). An extensive 2010 meta-analysis, including over 17,000 patients, suggests this variant does not significantly influence coronary artery disease risk. This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 pos...
Frequency: 52.3%
References:6
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
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[OMIM:ERBB2 POLYMORPHISM]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
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[PharmGKB:Curated A study on 50 subjects (25 patients who developed a distinct hearing loss during cisplatin therapy and in 25 patients without hearing impairment after cisplatin therapy)observed a higher frequency of the A-allele of rs2075252 in the LRP2 in the group with hearing impairment than in the group with normal hearing after cisplatin therapy.]
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common form...
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[PharmGKB:Curated The G allele of this SNP is associated with increased incidence of medium-severe nausea or vomiting, and with reduced leukocyte counts in gastric carcinoma and colon carcinoma patients treated with 5-fluorouracil. The elimination constant (Ke) for 5-fluorouracil was significantly lower in patients homozygous for the G allele.]
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[PharmGKB:Curated Risk or phenotype-associated allele: T allele. Phenotype: The T allele of rs3130690 (36 kb telomeric to HLA-B), which is strongly associated with the HLA-B*1502 allele, shows strong association with carbamazepine (CBZ)-induced Stevens-Johnson syndrome (SJS)/Toxic Epidermal Necrolysis (TEN, Lyell's syndrome) (OR = 254.6 for TT/TG genotype versus GG genotype; T allele only: p = 4.66x10(-42), Pc = 1.29x10(-39), OR = 45.65). Also, an extended haplotype with rs3130690 T, HLA-B*1502, and other alleles of major histocompatibility complex genes (A*1101-Cw*0801-HLABC-CA*119-rs3130690T-B*1502-MICA*019-DRB1*1202) was in strong association with CBZ-induced SJS/TEN. Study size: 204. Study population/ethnicity: 60 CBZ-induced SJS/TEN cases and 144 CBZ-tolerant controls of Chinese desce...
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rs12762549 and rs11045585 can be used to predict whether docetaxel will induced leukopenia/neutropenia, according to a study of ~100 Japanese patients. When patients were classified into three groups by the scoring system based on the genotypes of these two SNPs, patients with a score of 1 or 2 were shown to have a significantly higher risk of docetaxel-induced leukopenia/neutropenia as compared to those with a score of 0 (P = 0.0000057; odds ratio [OR], 7.00; 95% CI [confidence interval], 2.95-16.59). This prediction system correctly classified 69.2% of severe leukopenia/neutropenia and 75.7% of non-leukopenia/neutropenia into the respective categories. [PharmGKB:Curated In a case control study using samples from BioBank Japan, the G allele of rs12762549 was associated with docetaxel-ind...
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[PharmGKB:Curated Risk or phenotype-associated allele: G allele. Phenotype: The G allele of rs1264511 shows strong association with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.001685, OR = 3.13. Type of association: GN; PD; TOX; ADR.]
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[PharmGKB:Curated The Ala (C) allele of this SNP is associated with grade 3 to 4 neutropenia and diarrhea and is an independent predictor of diarrhea in patients with colorectal neoplasms.]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*3, defined as the common loss of function variant rs1057910(C) (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/. Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of nonsteroidal anti-inflammatory drugs (NSAIDs) that are CYP2C8 or CYP2C9 substrates, such as aceclofena...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
normal
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rs351855, a SNP in the fibroblast growth factor receptor 4 (FGFR4) gene, is also known as the Gly388Arg variant. The rs351855(T) allele encodes the risk (Arg) allele. The Arg form of this SNP is likely to cause a harder to treat version of node-positive breast cancer, including reducing the efficacy of Herceptin, based on a study of 372 patients. A study of ~500 Japanese prostate cancer patients found that individuals with a rs351855(T;T) genotype had a 2.2- and 1.9-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 1.8-fold increased risk of metastatic prostate cancer compared to the (C;C) genotype. A meta-analysis published in 2011, surveying a total of 2,618 cases of prostate cancer, concluded that the odds ratio per rs351855(T) allele was 1.17 (CI: 1.07...
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rs7569963 is directly adjacent to CREB1. Associated with significantly (p = 0.005) increased chance of suicide in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males, p = 0.009 [PharmGKB:Curated In a nested case-control study derived from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study this SNP in the CREB1 gene was associated with treatment-emergent suicidality among men with depression.]
common in clinvar
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer * cleft lip and cleft palate * coronary artery disease * depression * hyperhomocysteinemia * migraine * neural tube defects * pre-eclampsia (ges...
normal risk
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rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also Anxiety Blog posting [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Patients with the 5-HTR2A intron 2 (rs7997012) AA genotype suffered from more pronounced side effects compared to carriers of the GA or GG genotype. Study size: 124. Study population/ethnicity: Caucasian; Patients with psychiatric diso...
normal
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
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rs2227956 in HSP70-hom, resulted in a significant association with noise-induced hearing loss [PharmGKB:Curated The C allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.] [OMIM:?]
normal
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This SNP, located in an intron of the GRIA3 gene (also known as AMPA3), has been linked in one study to increased thoughts of suicide in patients taking the anti-depressant drug citalopram. The increased risk is calculated to be 1.9x. If the individual is also carrying two rs2518224(C) alleles, i.e. is a rs2518224(C;C) homozygote, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIA3 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
normal
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rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well by the variant OATP1B1 protein encoded by the rs4149056(C) allele include: *Several cholesterol lowering statins, generally leading to reduced inh...
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
7x less likely to respond to certain antidepressants
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rs2032583 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
normal
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This SNP, located in an intron of the GRIK2 gene, has been linked in one study to increased thoughts of suicide in patients using the anti-depressant drug citalopram. The risk is only seen for individuals carrying two rs2518224(C) alleles, i.e. the rs2518224(C;C) homozygotes. The odds ratio for these individuals is 8.2. If the individual also has at least one rs4825476(G) allele, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIK2 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
normal
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rs6413419, also known as 4768G>A or V179I, is a SNP in the CYP2E1 gene. The rs6413419(A) allele defines the CYP2E1*4 variant.
common in complete genomics
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23andMe reports that the T allele of rs3918290 is associated with the rare recessive disorder dihydropyrimidine dehydrogenase deficiency (DPD), also known as hereditary thymine-uraciluria or familial pyrimidinemia. pharmgkb - defines *2A allele, which has a significantly higher chance of 5-fluorouracil toxicity Fluorouracil Toxicity [PharmGKB:In-Depth Heterozygosity for the A allele of this SNP is associated with mucositis and leukopenia drug toxicity in cancer patients treated with fluorouracil. Heterozygous males were more likely than heterozygous females to develop severe toxicity. In this study, no A/A homozygotes were observed.]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
common
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This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an Apo-ε4 allele. The Apo-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between the...
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
more likely to gain weight if taking olanzapine
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and o...
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common
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This SNP encodes a variation in the 33rd amino acid of the protein encoded by the TBX21 gene. Although 95% or so of all Caucasians carry two copies of the rs2240017(G) allele, as oriented in dbSNP orientation, and are thus rs2240017(G;G) homozygotes, a few individuals are rs2240017(C;G) heterozygotes. These heterozgotes are reported to improve better over time in response to corticosteroid treatment for asthma than the rs2240017(G;G) homozygotes. So far, studies have not linked, however, this SNP to any change in the overall risk of asthma itself. Although the effect observed was strong, in that treating rs2240017(C;G) heterozygotes ultimately (over 4 years) yields average airway responsiveness in the normal range (i.e. in the same range as for nonasthmatics), the authors point out that th...
more responsive to statin treatment
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rs17244841, also known as SNP 12, is located in the HMG-CoA reductase HMGCR gene. The protein encoded by this gene is the target for drugs designed to inhibit its action, in order to lower cholesterol levels. SNPs in the HMGCR gene may affect how well such drugs (typically statins) work. In a study of ~1,500 patients treated with 40mg/d of pravastatin, rs17244841(A;T) heterozgyotes had a mean decrease in total cholesterol of –32.8 mg/dL (–0.85 mmol/L), while the mean change for rs17244841(A;A) homozygotes was –42.0 mg/dL (–1.09 mmol/L), a reduction in overall efficacy of 21.8% (absolute difference, 9.2 mg/dL, CI: 3.8-14.6 mg/dL, p=.001). The drop in total cholesterol was almost completely due to the decrease in LDL cholesterol, as there was no significant difference in the change i...
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
51 snps
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mix of muscle types this genotype indicate somewhat impaired muscles
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
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[PharmGKB:Curated The -58C allele of the human beta2 bradykinin receptor gene has been associated with hypertension in a Chinese Han population and an African American population.]
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[OMIM:UNCOUPLING PROTEIN 3; UCP3]
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Vascular endothelial growth factor gene polymorphisms in Behcet's disease. A functional variant of vascular endothelial growth factor is associated with severe ischemic complications in giant cell arteritis. Analysis of vascular endothelial growth factor (VEGF) functional variants in rheumatoid arthritis. Association between functional haplotypes of vascular endothelial growth factor and renal complications in Henoch-Schonlein purpura. Polymorphisms in the vascular endothelial growth factor gene and breast cancer in the Cancer Prevention Study II cohort. Vascular endothelial growth factor gene haplotypes in Kawasaki disease. Functional variation in VEGF is not associated with type 2 diabetes in a United Kingdom Caucasian population. VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic...
normal
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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Associated with baseline cholesterol levels in a study of 9,000+ individuals in Washington County, Maryland. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs2016520 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0056 Type of association: PD; CO]
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
common in complete genomics
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suggesting a positive association between the AG genotype, and possibly the G allele, and the likelihood of being an elite endurance athlete perhaps similar to rs1815739 NRF2 genotype improves endurance capacity in response to training.
10 snps
(hide) Eye color
Magnitude: 2.5
According to this is blue eye color haplotype #3, however user self reporting suggests it is not a reliable predictor of eye color.
Magnitude: 2.3
thumb|light brown gs255 eyes According to this is Blue eye color haplotype #1, however numerous caucasian users have self reported brown eyes.It is clearly not the darker eye color found in asian or african populations, but it also is not particularly predictive of a reliable eye color. thumb|light blue gs255 eyes thumb|gray blue gs255 eyes
blond hair & blue eyes is 4x more likely
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rs1667394 increases susceptibility to Blond rather than brown hair 4.94 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than brown eyes 29.43 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than green eyes 6.74 times for carriers of the A allele For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:Eye color]
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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[GWAS:Eye color traits]
Frequency: 20.0%
References:1
References:1
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[GWAS:None]
Frequency: 31.0%
References:9
References:9
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associated with hair color rs12896399 rs12203592 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER] [GWAS:Black vs. blond hair color]
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[GWAS:Eye color]
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eye color [GWAS:Eye color]
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[GWAS:None]
Frequency: 40.7%
References:0
References:0
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Influences appearance gnxp
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[GWAS:Eye color]
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[GWAS:Eye color traits]
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/table/pgen-1000934-t002/
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eye color http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/table/pgen-1000934-t002/ Digital quantification of human eye color highlights genetic association of three new loci.
blue eye color if part of blue eye color haplotype
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rs4778241 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variatio...
blue eye color if part of blue eye color haplotype
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rs916977 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [PharmGKB:Non-Curated GWAS results: Three genome-wide association studies and a linkage analysis identify H...
blue eye color if part of blue eye color haplotype
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rs3935591 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940272(C) rs8028689(T) rs2240203(A) rs11631797(G) rs916977(G)
blue eye color if part of blue eye color haplotype
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rs7183877 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
Frequency: 89.4%
References:1
References:1
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[GWAS:Eye color]
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
brown eye color more likely
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rs1129038 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:None]
brown/black eyes more likely
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
Magnitude: 0
Frequency: 3.5%
References:29
Frequency: 3.5%
References:29
brown eye color, 80% of the time observed in User:Watson and User:Dichro
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rs12913832 is a SNP near the OCA2 gene that may be functionally linked to blue or brown eye color, due to a lowering of promoter activity of the OCA2 gene. Blue eye color is associated with the rs12913832(G;G) genotype. For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). rs12913832 is also part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, that is found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other racial groups. rs12913832-T (brown eye) homozygotes compared to rs12913832-C (blue eye). correlations with skin,...
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
common on affy axiom data
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23andMe blog rs1393350 A 1.29 Melanoma rs1393350 increases susceptibility to Blond rather than brown hair 1.29 times for carriers of the A allele rs1393350 increases susceptibility to Blue rather than green eyes 1.52 times for carriers of the A allele rs1393350 increases susceptibility to Skin sensitivity to sun 1.26 times for carriers of the A allele A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Digital quantification of human eye color highlights genetic association of three new loci. [OMIM:TYROSINASE; TYR] [GWAS:Tanning]
Magnitude: 0
Frequency: 70.8%
Repute:Good
References:18
Frequency: 70.8%
Repute:Good
References:18
common on affy axiom data
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plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent associated with hair color rs12896399 rs12203592 rs12203592 for freckling was previously associated with hair color, eye color, and tanning response to sunlight Squamous Cell Carcinoma [PharmGKB:Non-Curated GWAS Results: A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation (Initial Sample Size: 2,287 women; Replication Sample Size: up to 8,465 individuals; Risk/trait Allele: rs12203592-T). This variant is associated with Black vs. red hair color.] [GWAS:Eye color] [GWAS:Black vs. red hair color]
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
blue eye color more likely
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rs12593929 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozgyous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
blue eye color more likely
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rs2240203 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
blue eye color if part of blue eye color haplotype
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rs8028689 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [GWAS:Multiple myeloma (IgH translocation)]
blue/gray eyes more likely
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rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page. [PharmGKB:Curated A haplotype containing rs11855019, rs6497268 and rs7495174 was highly associated with eye color, hair color and skin pigmentation in a mostly Northern European twin study.] [OMIM:OCA2 GENE]
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
generally non-European, but if European, 7x more likely to have black hair
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pi...
2 genosets 37 snps
(hide) Finnish
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GRACILE syndrome is a very rare metabolic disorder that affects newborn infants of Finnish ancestry.
1 snp
(hide) Folate
2.90 ng/mL lower Vitamin B6 blood concentration
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Genetics and genomics of human ageing. [PharmGKB:Non-Curated The C allele of this SNP is associated with lower blood concentration of vitamin B6 (Combined studies of Tuscan Italians ( inCHIANTI:N =1175 and Progetto Nutrizione study:N = 687) found 1.45 ng/mL lower vitamin B6 per copy of C (p = 8.3 x 10 (-18)))] [OMIM:?] [GWAS:Folate pathway vitamins]
Frequency: 35.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 10p13; Reported Gene(s): CUBN; Risk Allele: rs11254363-A); (p-value= 0.000001).This variant is associated with Folate pathway vitamins.] [GWAS:Folate pathway vitamins]
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 19q13.33; Reported Gene(s): FUT2; Risk Allele: rs602662-A); (p-value= 3E-20).This variant is associated with Folate pathway vitamins.] [OMIM:VITAMIN B12 PLASMA LEVEL QUANTITATIVE TRAIT LOCUS 1; B12QTL1] [GWAS:Folate pathway vitamins]
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rs1076991 C > T exerts a significant effect on promoter activity in vitro and along with rs2236225 G > A influences embryonic development. Common genetic polymorphisms affect the human requirement for the nutrient choline. Neural tube defects and folate pathway genes: family-based association tests of gene-gene and gene-environment interactions. Gene response elements, genetic polymorphisms and epigenetics influence the human dietary requirement for choline. Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not. Folate and one-carbon metabolism gene polymorphisms and their associations with oral facial clefts. Association of polymorphisms in one-carbon metabolizing genes and lung cancer risk: a case-cont...
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Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway. G allele associated with lower serum Vitamin B12. 'The TCN1 rs526934 G variant may reduce transport of cobalamin, resulting in lower plasma vitamin B12 levels.' [PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 11q12.1; Reported Gene(s): TCN1; Risk Allele: rs526934-A); (p-value= 0.000002).This variant is associated with Folate pathway vitamins.] [GWAS:Folate pathway vitamins]
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rs1051266 (Arg27Cys, 80G>A) is a snp within SLC19A1 (Solute carrier family 19 (folate transporter), member 1). Cys (A) allele associated with reduced plasma folate women with GA and AA genotypes had higher red blood cell folate concentrations, not significantly associated with serum folate or homocysteine levels methotrexate (antifolate drug) uptake lowest in individuals with GG genotype than those with GA or AA genotypes [PharmGKB:Curated Risk or phenotype-associated allele: SLC19A1 80GG (27Arg/Arg) and GA (27His/Arg)>AA (27His/His) genotypes. Phenotype: A composite pharmacogenetic index (additive from zero to five) was calculated using the following values: ATIC 347CC or TSER*3/*3 or SLC19A1 80GG or SLC19A1 80GA genotypes were valued as 0, ATIC 347CG or TSER*2/*3 or SLC19A1 80AA g...
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 3p14.1; Reported Gene(s): PRICKLE2; Risk Allele: rs153734-T); (p-value= 0.000007).This variant is associated with Folate pathway vitamins.] [GWAS:Folate pathway vitamins]
common in clinvar
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer * cleft lip and cleft palate * coronary artery disease * depression * hyperhomocysteinemia * migraine * neural tube defects * pre-eclampsia (ges...
8 snps
(hide) Forensically Useful Morphological Traits
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 journal LDL-Cholesterol minor allele was associated with up to 2.2-fold lower expression Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Analysis of recently identifie...
brown/black eyes more likely
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
normal
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rs2297480 is a SNP in the FDPS gene, which encodes an enzyme in the mevalonate pathway and therefore might alter the response to amino-bisphonate (drug) treatment of postmenopausal osteoporosis. A study of 234 Danish postmenopausal women treated for at least 2 years with amino-bisphonates concluded that rs2297480(C;C) homozygotes do not respond as successfully as (A;A) or (A;C) genotypes. [PharmGKB:Curated This variant impacted the response to long-term N-bisphosphonates treatment in a study of 234 Danish postmenopausal women. Patients with the homozygous CC genotype showed a decreased response of bone turnover markers to amino-bisphosphonate therapy.]
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
common in clinvar
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rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair color in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also OMIM 155555.0006 [OMIM:?]
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
common in clinvar common for Caucasians on the 23andme platform
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rs2228479, known as Val92Met or V92M, is one of several SNPs in the MC1R gene commonly associated with red (or blond) hair and poor tanning, but note its high presence in one Asian population The risk allele is rs2228479(A), compared with the wild-type rs2228479(G) allele. See also OMIM 155555.0002 [OMIM:?]
normal
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Although the rs26722(T) alllele is relatively rare, at least statistically it seems to be associated with darker eye, hair, and skin color, all other things being equal. A genomewide association study of skin pigmentation in a South Asian population. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Association of the SLC45A2 gene with physiological human hair colour variation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Genetic determinants of hair and eye colours in the Scottish and Danish populations. [OMIM:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
common in complete genomics
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A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. [GWAS:Tanning]
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
common in complete genomics
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rs1805006, known as Asp84Glu or D84E, is one of several SNPs in the MC1R gene associated with higher risk of melanoma. The risk allele is rs1805006(A), compared with the wild-type rs1805006(C) allele. Allelic odds ratio for pale skin(P-value)=5.19(<1.0e-5)MC1R*D84E rs1805006 http://genepi.qimr.edu.au/contents/p/staff/Duffyetal_JID_520-528Jan10.pdf See also OMIM 155555.0003 [OMIM:?]
18 snps
(hide) Freckling
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
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An association between freckling and rs2153271 [GWAS:Freckling]
None
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
Magnitude: 0
Frequency: 70.8%
Repute:Good
References:18
Frequency: 70.8%
Repute:Good
References:18
common on affy axiom data
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plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent associated with hair color rs12896399 rs12203592 rs12203592 for freckling was previously associated with hair color, eye color, and tanning response to sunlight Squamous Cell Carcinoma [PharmGKB:Non-Curated GWAS Results: A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation (Initial Sample Size: 2,287 women; Replication Sample Size: up to 8,465 individuals; Risk/trait Allele: rs12203592-T). This variant is associated with Black vs. red hair color.] [GWAS:Eye color] [GWAS:Black vs. red hair color]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
8 snps
(hide) French-Canadian
normal
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omim 131240 In a study of 103 candidate genes for coronary artery disease and associated phenotypes in the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, Pare et al. (2007) found that HDL cholesterol levels were associated with a lysine-to-asparagine substitution at codon 198 (K198N) of the EDN1 gene in a sex-specific manner. The minor allele T (Asn) of the K198N substitution (dbSNP rs5370) was associated with lower HDL cholesterol values. Women showed a strong association between dbSNP rs5370 and HDL cholesterol (P = 1.3 x 10(-5)), whereas in men no such significant association was identified (P = 0.14). 3x increase in the adjusted odds of being hypertensive of rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, 9CI: 1.02 - 8.19). Afte...
normal risk
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-related gene polymorphi...
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Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a neurodegenerative disorder first described in French-Canadian individuals from the Charlevoix and Saguenay-Lac-St-Jean regions of northeastern Quebec. Symptoms begin in early childhood and typically involve muscle overactivity and lack of muscle coordination, resulting in difficulty walking, moving the limbs, and speaking. https://www.23andme.com/you/journal/arsacs/overview/
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Leigh syndrome is more common in some French-Canadian populations. [OMIM:LEIGH SYNDROME DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
4 snps
(hide) GCH1
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A GCH1 Haplotype Associated with Susceptibility to Vasoocclusive Pain and Impaired Vascular Function in Sickle Cell Anemia
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Polymorphic Variation of the Guanosine Triphosphate Cyclohydrolase 1 Gene Predicts Outcome in Patients Undergoing Surgical Treatment for Lumbar Degenerative Disc Disease Lack of influence of GTP cyclohydrolase gene (GCH1) variations on pain sensitivity in humans. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? T allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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Polymorphic Variation of the Guanosine Triphosphate Cyclohydrolase 1 Gene Predicts Outcome in Patients Undergoing Surgical Treatment for Lumbar Degenerative Disc Disease
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. C allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. C allele associated with higher tolerance to pain.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. T allele associated with higher tolerance to pain.
Frequency: 79.7%
References:1
References:1
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Polymorphic Variation of the COMT and GCH1 Genes In Patients Undergoing Surgical Treatment For Lumbar Degenerative Disc Disease Lack of influence of GTP cyclohydrolase gene (GCH1) variations on pain sensitivity in humans.
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[GWAS:None]
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Do genetic predictors of pain sensitivity associate with persistent widespread pain? C allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. A allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. A allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? A allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
Magnitude: 0
Frequency: 75.0%
References:0
Frequency: 75.0%
References:0
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A GCH1 Haplotype Associated with Susceptibility to Vasoocclusive Pain and Impaired Vascular Function in Sickle Cell Anemia
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Also known as Lys224Arg, G allele is associated with Dopa-Responsive Dystonia. Dystonia with motor delay in compound heterozygotes for GTP-cyclohydrolase I gene mutations. Dopa-responsive dystonia in British patients: new mutations of the GTP-cyclohydrolase I gene and evidence for genetic heterogeneity. Autosomal dominant GTP-CH deficiency presenting as a dopa-responsive myoclonus-dystonia syndrome. [OMIM:?]
13 snps
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One copy of H63D, carrier of hemochromatosis, likely unaffected unless also C282Y carrier. You are a carrier for rs1799945(G) H63D Hereditary hemochromatosis. You are unlikely to be affected unless also a carrier of rs1800562(A) C282Y, but others in your family may be. This is a treatable condition.
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rs1799945 represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutations are commonly found in people with Eu...
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[GWAS:Hemoglobin levels]
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
common in clinvar
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer * cleft lip and cleft palate * coronary artery disease * depression * hyperhomocysteinemia * migraine * neural tube defects * pre-eclampsia (ges...
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who actually develop...
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
Magnitude: 0
Frequency: 98.4%
Repute:Good
References:7
Frequency: 98.4%
Repute:Good
References:7
common in clinvar
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The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. 23andMe tests for SNPs in the MEFV gene that are associated with a recessive form of familial Mediterranean fever: * rs28940579, also known as V726A (risk allele G) * rs28940580, also known as M680I C>G (risk allele G) * rs28940578, also known as M694I (risk allele T) * rs3743930, also known as E148Q (risk allele G) * rs11466023, also known as P369S (risk allele A) * i4000406, also known as M694V (risk allele C) * i4000409, also known as A744S (risk allele A) * i4000403, also known as F479L (risk allele C) * i4000410, also known as R761H (risk allele T) * i40...
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:9
Frequency: 99.1%
Repute:Good
References:9
normal
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[PharmGKB:Curated This variant is associated with risk of pancreatitits for HIV-infected individuals.] [OMIM:PANCREATITIS, CHRONIC, SUSCEPTIBILITY TO]
common in clinvar
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[PharmGKB:Curated In a study of pediatric malaria treatments in Africa, patients with G6PD deficiency, as assessed by the G6PD:202G>A variant, showed a higher risk of severe anaemia following treatment with chlorproguanil-dapsone plus artesunate.] [OMIM:G6PD ASAHI]
common in clinvar
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Profound biotinidase deficiency in two asymptomatic adults. Partial biotinidase deficiency is usually due to the D444H mutation in the biotinidase gene. Mutations causing profound biotinidase deficiency in children ascertained by newborn screening in the United States occur at different frequencies than in symptomatic children. [OMIM:?]
14 snps
(hide) Gs240
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mentioned by gs240
Frequency: 22.1%
References:3
References:3
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Haplotype rs12740310*C-rs3737296*G-rs12410279*A was overtransmitted (p(corrected)=0.0016), with a relative risk for autism of 1.8 in homozygous carriers [OMIM:MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1; MARK1]
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rs7766973 is a SNP in the jumonji, AT rich interactive domain 2 JARID2 gene. Significantly (p = 2 x 10e-7) but weakly associated with autism based on a GWAS study of 1,000+ affected families. However, upon attempted replication, rs7766973 did not meet genome-wide significance. Nonetheless, a French company (Integragen) announced in 2011 (that is was licensing the use of this SNP for identifying children at increased risk for autism, perhaps by combining rs7766973] with other autism-related SNPs.
Frequency: 69.7%
References:3
References:3
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mentioned by gs240
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
slightly increased risk for autism
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A common SNP in the CNTNAP2 gene, rs7794745, is associated with increased risk for autism based on a study of 148 affected children from families with two more autistic children. Related article A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Do candidate genes discriminate patients with an autism spectrum disorder from those with attention deficit/hyperactivity disorder and is there an effect of lifetime substance use disorders? A common genetic variant in the neurexin superfamily member CNTNAP2 is associated with increased risk for selective mutism and social anxiety-related traits. Genetic variation in CNTNAP2 alters brain function during linguistic processing in healthy individuals. [PharmGKB:Curated This common variant in CNTNAP2 is significantl...
average
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin use. A protective effect of rs5918 has also been observed for the development of Non-Hodgkin Lymphoma, both...
7 snps
(hide) Gs247
highest risk rs10513789(T;T) increased risk of developing Parkinson's Disease see also gs249 for the more common heterozygote form http://www.genomicslawreport.com/index.php/2012/06/01/patenting-and-personal-genomics-23andme-receives-its-first-patent-and-plenty-of-questions/
Magnitude: 2
Frequency: 55.8%
Repute:Bad
References:1
Frequency: 55.8%
Repute:Bad
References:1
very common, but higher risk of Parkinson's disease approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease. It is notable because it is the first snp patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
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[GWAS:None]
Frequency: 24.8%
References:4
References:4
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Genomewide association study for susceptibility genes contributing to familial Parkinson disease. A unified framework for multi-locus association analysis of both common and rare variants. [GWAS:Parkinson's disease]
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People with two copies of the T allele at rs6812193 appear to have a slightly lower risk of Parkinson's disease. The same researchers identified another risk allele for Parkinson's disease at rs11868035. plos [GWAS:Parkinson's disease]
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Mentioned in the 23andMe Parkinson's disease patent along with rs10513789
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Mentioned in the 23andMe Parkinson's disease patent along with rs10513789
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[GWAS:None]
1 genoset 7 snps
(hide) Gs248
Magnitude: 2
Frequency: 55.8%
Repute:Bad
References:1
Frequency: 55.8%
Repute:Bad
References:1
very common, but higher risk of Parkinson's disease approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease. It is notable because it is the first snp patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
Frequency: 82.3%
References:0
References:0
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see gs248 patented by 23andMe to diagnose Parkinson's disease
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
3 snps
(hide) Gs249
highest risk rs10513789(T;T) increased risk of developing Parkinson's Disease see also gs249 for the more common heterozygote form http://www.genomicslawreport.com/index.php/2012/06/01/patenting-and-personal-genomics-23andme-receives-its-first-patent-and-plenty-of-questions/
Magnitude: 2
Frequency: 55.8%
Repute:Bad
References:1
Frequency: 55.8%
Repute:Bad
References:1
very common, but higher risk of Parkinson's disease approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease. It is notable because it is the first snp patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
1 genoset 1 snp
(hide) Gs250
Magnitude: 2
Frequency: 55.8%
Repute:Bad
References:1
Frequency: 55.8%
Repute:Bad
References:1
very common, but higher risk of Parkinson's disease approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease. It is notable because it is the first snp patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
1 snp
(hide) Hair
straighter hair
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rs11803731, a SNP in the Trichohyalin gene (TCHH) gene, is estimated to account for 6% of the variance in hair morphology (ie hair curliness) based on a study of Australians of European ancestry. [OMIM:?] [GWAS:Hair morphology]
Frequency: 15.9%
References:1
References:1
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[GWAS:Hair morphology]
Frequency: 30.1%
References:1
References:1
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[GWAS:Hair morphology]
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[GWAS:Hair morphology]
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[GWAS:Hair morphology]
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[GWAS:Hair morphology]
Frequency: 63.1%
References:1
References:1
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[GWAS:Hair morphology]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:1
Frequency: 92.0%
Repute:Good
References:1
12 snps
(hide) Hair color
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
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[GWAS:Hair color]
Frequency: 31.0%
References:9
References:9
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associated with hair color rs12896399 rs12203592 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER] [GWAS:Black vs. blond hair color]
Frequency: 32.1%
References:1
References:1
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[GWAS:Hair color]
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[GWAS:Hair color]
Magnitude: 0
Frequency: 71.7%
References:8
Frequency: 71.7%
References:8
normal
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A 2007 study based on the Icelanders and Dutch concluded that individuals with an rs12821256(C) allele were ~2x fold more likely to have blond than brown hair color. The specific odds ratio claimed is 2.32, p = 5.5 x 10<sup>-14</sup>. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with blond vs. brown hair.] [OMIM:KIT LIGAND; KITLG] [GWAS:Hair color] [GWAS:Blond vs. brown hair]
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
common in clinvar
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rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair color in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also OMIM 155555.0006 [OMIM:?]
Magnitude: 0
References:0
References:0
normal
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This missense mutation influences red hair color and has been observed in the Spanish maternal ancestry of User:Corpas son.
generally non-European, but if European, 7x more likely to have black hair
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pi...
13 snps
(hide) Hair curliness
straighter hair
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rs499697 the minor, derived allele is associated with curlier hair curl, 0.13 points per G. [GWAS:Common traits (Other)]
straighter hair
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rs11803731, a SNP in the Trichohyalin gene (TCHH) gene, is estimated to account for 6% of the variance in hair morphology (ie hair curliness) based on a study of Australians of European ancestry. [OMIM:?] [GWAS:Hair morphology]
Magnitude: 0
Frequency: 61.3%
References:2
Frequency: 61.3%
References:2
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rs17646946 is a SNP on chromosome 1 that is apparently part of the trichohyalin-like 1 TCHHL1 gene. Trichohyalin is a protein found in hair follicle roots. In an interesting example of people-powered research, this SNP and one other were reported to be associated with hair curliness. Source: hair curl rs17646946 and rs7349332. source genetic future rs17646946 and hair curl with each A conferring a reduction in curliness of about 0.29 points on a scale from 0 to 5. See also: rs11803731 [GWAS:Common traits (Other)]
straighter hair
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hair curl rs17646946 and rs7349332. source genetic future Appearance [GWAS:Common traits (Other)]
4 snps
(hide) Haplogroup I (Y-DNA)
P30-
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The i4000178(A;A) mutation is a reliable indicator of Haplogroup I1 (Y-DNA) subclade of Haplogroup I (Y-DNA) and is also referred to as P30+. [haplogroup:?]
P38+ Match for haplogroup I (Y-DNA). [haplogroup:I (Y-DNA)]
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The i4000186(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as P38+. [haplogroup:?]
U179-
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The rs2319818(A;A) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as U179+. [haplogroup:?]
M258-
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The rs9341301(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as M258+. [haplogroup:?]
M170- M170-
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Also known as M170. The rs2032597(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as M170+. Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
5 snps
(hide) Haplogroup R1b1b2g (Y-DNA)
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dna-forums rs2032634 (M73) was known to be wrong for most of the 23andMe v1 results [haplogroup:?]
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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gs252 [haplogroup:?]
common on affy axiom data common for Caucasians on the 23andme platform
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[haplogroup:?]
8 snps
(hide) Haplogroup Y (Y-DNA)
Frequency: 3.4%
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
Frequency: 34.5%
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
Frequency: 69.0%
References:0
References:0
Frequency: 69.0%
References:0
References:0
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[haplogroup:?]
Frequency: 69.0%
References:0
References:0
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[haplogroup:?]
Frequency: 69.0%
References:0
References:0
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[haplogroup:?]
[haplogroup:R]
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Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
Frequency: 93.1%
References:0
References:0
Frequency: 96.6%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
(hide)
[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
It indicates a particular branch in asian ancestry, but also turns up commonly in europeans where it can be ignored. [haplogroup:O3]
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
[haplogroup:F-R]
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In silico and in vitro comparative analysis to select, validate and test SNPs for human identification. MEGF10 association with schizophrenia. FBXL21 association with schizophrenia in Irish family and case-control samples. Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
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[haplogroup:?]
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MEGF10 association with schizophrenia. FBXL21 association with schizophrenia in Irish family and case-control samples. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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dna-forums rs2032634 (M73) was known to be wrong for most of the 23andMe v1 results [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
Testing a feature. This genotype is called (I;I) by 23andMe. SNPedia thinks of it as (G;G).
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
U179-
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The rs2319818(A;A) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as U179+. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
References:0
References:0
References:0
(hide)
[haplogroup:?]
References:0
References:0
References:0
References:0
References:0
References:0
References:0
References:0
References:0
References:0
References:0
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
M258-
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The rs9341301(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as M258+. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
[haplogroup:P]
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In silico and in vitro comparative analysis to select, validate and test SNPs for human identification. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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23andMe discussion R1b large group splits for rs11799226 ; C is ancestral and G is derived . if you have G, please show up and sign here (geographical origin is welcome). http://www.familytreedna.com/public/R-L21/default.aspx ==Associated Genosets== {| class='wikitable sortable' |+ Haplogroup R1b1b2a1a2f and Subclades |- ! Haplogroup ! Parent Haplogroup ! Publication ! Defining SNPs ! 23andMe Genoset ! deCodeMe Genoset ! Full Genomic Sequence (FTDNA and Argus Bio) |- |R1b1b2a1a2f1 ||R1b1b2a1a2f || || M37 (private, 23andMe) || || || |- |R1b1b2a1a2f2 ||R1b1b2a1a2f || || M222/USP9Y+3636 || gs214 || || |- |R1b1b2a1a2f3 ||R1b1b2a1a2f || || P66 (private) || || || |- |R1b1b2a1a2f4 ||R1b1b2a1a2f || || L226/S168 || || || |- |R1b1b2a1a2f5 ||R1b1b2a1a2f || || L193/S176 || || || |}
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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Genetic variants of Y chromosome are associated with a protective lipid profile in black men. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
M170- M170-
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Also known as M170. The rs2032597(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as M170+. Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
Magnitude: 0
Frequency: 96.6%
References:0
Frequency: 96.6%
References:0
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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gs252 [haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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[haplogroup:?]
common for Caucasians on the 23andme platform
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This SNP also goes under the name M174. As such, it has been recognized as one of the most reliable indicators of Y haplogroup D. The mutation from T to C indicates membership of the Asian haplogroup D. [haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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[haplogroup:?]
325 snps
(hide) Haplogroups
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haplogroups
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haplogroups
Frequency: 3.4%
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
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haplogroups
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[haplogroup:?]
Frequency: 34.5%
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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haplogroups ,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=G |derived_allele=A }}
Frequency: 69.0%
References:0
References:0
Frequency: 69.0%
References:0
References:0
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[haplogroup:?]
Frequency: 69.0%
References:0
References:0
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[haplogroup:?]
Frequency: 69.0%
References:0
References:0
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[haplogroup:?]
[haplogroup:R]
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Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
Frequency: 96.6%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
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It indicates a particular branch in asian ancestry, but also turns up commonly in europeans where it can be ignored. [haplogroup:O3]
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
[haplogroup:F-R]
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In silico and in vitro comparative analysis to select, validate and test SNPs for human identification. MEGF10 association with schizophrenia. FBXL21 association with schizophrenia in Irish family and case-control samples. Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H4 |ancestral_allele=G |derived_allele=A }}
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1c |derived_haplogroup=H1c1 |ancestral_allele=A |derived_allele=G }}
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haplogroups
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haplogroups
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haplogroups same SNP as rs28358282 ,Achilli 2004 ('H2c') |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a3 |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a4 |ancestral_allele=C |derived_allele=T }}
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H3 |derived_haplogroup=H3c |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H3 |derived_haplogroup=H3a |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1c |derived_haplogroup=H1c1 |ancestral_allele=T |derived_allele=G }}
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haplogroups ,Achilli 2004 ('H2c') |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a3 |ancestral_allele=G |derived_allele=A }}
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haplogroups
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haplogroups
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Haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2a1 |ancestral_allele=C |derived_allele=T }}
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a1 |ancestral_allele=G |derived_allele=A }}
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1a |derived_haplogroup=H1f |ancestral_allele=T |derived_allele=C }}
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haplogroups
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
P30-
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The i4000178(A;A) mutation is a reliable indicator of Haplogroup I1 (Y-DNA) subclade of Haplogroup I (Y-DNA) and is also referred to as P30+. [haplogroup:?]
P38+ Match for haplogroup I (Y-DNA). [haplogroup:I (Y-DNA)]
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The i4000186(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as P38+. [haplogroup:?]
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1a |derived_haplogroup=H1f |ancestral_allele=A |derived_allele=G }}
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1a |derived_haplogroup=H1f |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1c |derived_haplogroup=H1c2 |ancestral_allele=C |derived_allele=T }}
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haplogroups
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
References:0
References:0
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[haplogroup:?]
References:0
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
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[haplogroup:?]
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MEGF10 association with schizophrenia. FBXL21 association with schizophrenia in Irish family and case-control samples. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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dna-forums rs2032634 (M73) was known to be wrong for most of the 23andMe v1 results [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
Testing a feature. This genotype is called (I;I) by 23andMe. SNPedia thinks of it as (G;G).
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
U179-
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The rs2319818(A;A) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as U179+. [haplogroup:?]
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[haplogroup:?]
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haplogroups
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[haplogroup:?]
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
References:0
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[haplogroup:?]
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[haplogroup:?]
M258-
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The rs9341301(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as M258+. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
[haplogroup:P]
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In silico and in vitro comparative analysis to select, validate and test SNPs for human identification. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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Genetic variants of Y chromosome are associated with a protective lipid profile in black men. [haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
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[haplogroup:?]
common on affy axiom data
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haplogroups ,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=T |derived_allele=C }}
M170- M170-
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Also known as M170. The rs2032597(C;C) mutation is a reliable indicator of Haplogroup I (Y-DNA) and is also referred to as M170+. Association of Y chromosome haplogroup I with HIV progression, and HAART outcome. [haplogroup:?]
common on affy axiom data
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haplogroups ,,Shen 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H1 |ancestral_allele=G |derived_allele=A }}
common on affy axiom data
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haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H2 |ancestral_allele=G |derived_allele=A }}
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haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2a |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Frequency: 96.6%
References:0
Frequency: 96.6%
References:0
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[haplogroup:?]
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haplogroups
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haplogroups
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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gs252 [haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common on affy axiom data common for Caucasians on the 23andme platform
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[haplogroup:?]
common for Caucasians on the 23andme platform
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This SNP also goes under the name M174. As such, it has been recognized as one of the most reliable indicators of Y haplogroup D. The mutation from T to C indicates membership of the Asian haplogroup D. [haplogroup:?]
common on affy axiom data
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haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a2 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
References:1
References:1
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haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1 |derived_haplogroup=H1a |ancestral_allele=A |derived_allele=G }}
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[haplogroup:?]
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haplogroups
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haplogroups
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[haplogroup:?]
362 snps
(hide) HLA-B*1502
common in complete genomics
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Helps to identify HLA-B*1502 [PharmGKB:Curated Risk or phenotype-associated allele: allele 4. Phenotype: Combined alleles of rs3909184 (2) and rs2844682 (4) are tagging SNPs for HLA-B*1502 (0.011 allele frequency). Study size: 45. Study population/ethnicity: Unrelated Han Chinese from Beijing, China. Significance metric(s): Type of association: GN]
common
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Helps to identify HLA-B*1502 [PharmGKB:Curated Risk or phenotype-associated allele: allele 2. Phenotype: Combined alleles of rs3909184 (2) and rs2844682 (4) are tagging SNPs for HLA-B*1502 (0.011 allele frequency). Study size: 45. Study population/ethnicity: Unrelated Han Chinese from Beijing, China. Significance metric(s): Type of association: GN]
2 snps
(hide) HLA-B*5701
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
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rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
1 snp
(hide) Intelligence
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non sig. gwas, hit (p = 5 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 7.1%
References:1
References:1
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[GWAS:Cognitive performance]
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non sig. gwas, top hit for spatial working memory (SWM) 'between for 8 box stage' in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 1 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
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non sig. gwas, top hit for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 6 x 10^-6) principal component 1 (PC1) - CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 20.4%
References:2
References:2
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non sig. gwas, hit (p = 6 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 2 x 10^-6) - Immediate Story Recall [GWAS:Cognitive Performance]
Frequency: 23.9%
References:2
References:2
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non sig. gwas, hit (p = 3 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, top hit for rapid visual information processing (RVP) hit probability in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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[GWAS:Cognitive performance]
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non sig. gwas, hit (p = 3 x 10^-7) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 3 x 10^-6) - Digit Symbol [GWAS:Cognitive Performance]
Frequency: 27.7%
References:2
References:2
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non sig. gwas, hit (p = 5 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Frequency: 28.3%
References:1
References:1
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[GWAS:Cognitive performance]
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (G;G) genotype appeared to typically have a 4 point higher IQ than the (A;G) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324650, showed similar results to rs324640, and was in linkage disequilibrium (r2 = 0.90) with it.
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
Frequency: 29.2%
References:2
References:2
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non sig. gwas, hit (p = 5 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
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[GWAS:Cognitive performance]
Frequency: 30.1%
References:2
References:2
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, Similarities [GWAS:Cognitive test performance]
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 2 x 10^-7) for forward digit span [GWAS:Cognitive Performance]
Frequency: 32.7%
References:2
References:2
(hide)
non sig. gwas, hit (p = 4 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 8 x 10^-6) for spatial span (SSP) length in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, top hit for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery), noted as close to ME3 which has shown expression changes in a rat model of schizophrenia ( ) [GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 8 x 10^-6) for verbal recognition memory (VRM) free recall in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, Wide-Range Achievement Test [GWAS:Cognitive test performance]
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[GWAS:Cognitive performance]
Frequency: 37.2%
References:2
References:2
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, top hit for spatial recognition memory (SRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 38.9%
References:2
References:2
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for backwards digit span [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 7 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, top 25 GEE p-values, measure of attention and executive function [GWAS:Cognitive test performance]
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for spatial span (SSP) length in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
4+ IQ points for breastfeeding
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4+ IQ points for breastfeeding with the AA or AG genotypes Breastfeeding and IQ [GWAS:Response to statin therapy]
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non sig. gwas, hit (p = 9 x 10^-6) principal component 1 (PC1) - CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
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non sig. gwas, top 25 GEE p-values, visual memory and organization [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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intelligence related [PharmGKB:Curated Several studies showed an associaction of this SNP in DTNBP1 with schizophrenia and other psychotic disorders, including substance-induced psychosis]
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[GWAS:Cognitive performance]
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Rs1378810 is located in DNAJC13, a Hsp40 homolog. associated with an estimated 0.4% variance in g (p = 0.0007), from a sample (2650 children) within the Twins Early Development Study. The beneficial allele was T, and it is assumed to be oriented with respect to the positive strand (based on the affy genechip used). high LD with rs2133692 per HapMap data (with +Rs1378810(T;T) strongly matching with rs2133692(T;T)) cursory mention in [SciAm]
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non sig. gwas, hit (p = 3 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 6 x 10^-6) principal component 1 (PC1) - CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 6 x 10^-6) - Animals [GWAS:Cognitive Performance]
Frequency: 53.6%
References:2
References:2
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 3 x 10^-6) - Symbol Search [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
(hide)
non sig. gwas, top hit for spatial span (SSP) length in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 3 x 10^-6) - Animals [GWAS:Cognitive Performance]
(hide)
non sig. gwas, top 25 GEE p-values, visual memory and organization [GWAS:Cognitive test performance]
(hide)
[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
Frequency: 63.1%
References:1
References:1
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 7 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 3 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 8 x 10^-6) - Animals [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 1 x 10^-6) - Animals [GWAS:Cognitive Performance]
(hide)
non sig. gwas, top 25 GEE p-values, measure of attention and executive function [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 4 x 10^-6) for Test Trails A performance [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 8 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, top 25 GEE p-values, measure of attention and executive function [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 78.5%
References:2
References:2
(hide)
non sig. gwas, hit (p = 3 x 10^-6) for Controlled Oral Word Association (COWA) test performance [GWAS:Cognitive Performance]
Frequency: 79.6%
References:2
References:2
(hide)
non sig. gwas, hit (p = 3 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for spatial recognition memory (SRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 83.2%
References:2
References:2
(hide)
non sig. gwas, hit (p = 4 x 10^-7) for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-6) - Immediate Story Recall [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 7 x 10^-7) - Animals [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 4 x 10^-7) for backwards digit span [GWAS:Cognitive Performance]
(hide)
Mentioned in retracted non sig. gwas, hit (p = 1 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
Frequency: 91.7%
References:1
References:1
(hide)
[GWAS:Cognitive performance]
Frequency: 95.6%
References:1
References:1
(hide)
[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
References:1
(hide)
[GWAS:Cognitive performance]
The (G;G) genotype averages 2.84 PIQ points lower than (A;A) genotype and averages 2.8 PIQ points lower than (A;G) genotype
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in . The (A;A) genotype averaged 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ. rs363050 is in close linkage with rs353016, with r2 = 0.98, such that the rs363050(A) allele typically is linked to the rs353016(T) allele. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP). Measures of Intelligence
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In 2009, a large, multi-sample replication study failed to find any significant association with Intelligence for this or other SNPs in CHRM2 . Earlier work had observed that this snp (and perhaps its neighbors) influenced intelligence and alcohol dependence CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (...
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This is one of four SNPs in the first intron of the SNAP25 gene that have been correlated with increased intelligence based on studies of ~300 Caucasian subjects. In orientation to the dbSNP entry for this SNP, rather than as published, the (C;C) genotype averages ~2 PIQ points higher than the (C;T) genotype, which averages 2 PIQ points higher than the (T;T) genotype. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in . The (T;T) genotype averages several PIQ points higher than the (C;T) genotype, which averages several PIQ points higher than the (C;C) genotype. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
common in complete genomics
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non sig. gwas, top 25 GEE p-values, visual memory and organization [GWAS:Cognitive test performance]
common in clinvar
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Mentioned in a 23andMe discussion on intelligence. Synonymous Polymorphisms at Splicing Regulatory Sites are Associated with CpGs in Neurodegenerative Disease-Related Genes.
common in complete genomics
(hide)
non sig. gwas, hit (p = 8 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
common on affy axiom data
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 3 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
common on affy axiom data
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
Magnitude: 0
Frequency: 79.6%
Repute:Good
References:2
Frequency: 79.6%
Repute:Good
References:2
common on affy axiom data
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non sig. gwas, hit (p = 6 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 80.4%
Repute:Good
References:2
Frequency: 80.4%
Repute:Good
References:2
common on affy axiom data
(hide)
non sig. gwas, hit (p = 8 x 10^-6) for Controlled Oral Word Association (COWA) test performance [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 82.3%
Repute:Good
References:2
Frequency: 82.3%
Repute:Good
References:2
common on affy axiom data
(hide)
non sig. gwas, hit (p = 8 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
Magnitude: 0
Frequency: 83.1%
Repute:Good
References:2
Frequency: 83.1%
Repute:Good
References:2
common on affy axiom data
(hide)
non sig. gwas, top hit for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, top 25 GEE p-values, measure of attention and executive function [GWAS:Cognitive test performance]
Magnitude: 0
Frequency: 86.5%
Repute:Good
References:2
Frequency: 86.5%
Repute:Good
References:2
common on affy axiom data
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:2
Frequency: 86.7%
Repute:Good
References:2
common on affy axiom data
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 7 x 10^-6) for verbal recognition memory (VRM) free recall in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-8) for backwards digit span [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 2 x 10^-7) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 91.1%
Repute:Good
References:2
Frequency: 91.1%
Repute:Good
References:2
common in complete genomics
(hide)
non sig. gwas, hit (p = 7 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-6) - Animals [GWAS:Cognitive Performance]
common on affy axiom data
(hide)
non sig. gwas, top hit for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:2
Frequency: 93.8%
Repute:Good
References:2
common in complete genomics
(hide)
non sig. gwas, hit (p = 8 x 10^-7) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common on affy axiom data
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-7) - Animals [GWAS:Cognitive Performance]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
common in complete genomics
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 3 x 10^-6) - Animals [GWAS:Cognitive Performance]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
(hide)
rs174575, has been investigated with respect to increased intelligence in breastfed children but not yielded any clear result. *Although there was no difference in IQ linked to the SNP alone, breastfed children carrying one or two copies of rs174575(C) had a significant (6 point) increase in IQ compared to carriers of the same allele who were not breastfed. For children who were homozygous non-carriers, i.e. rs174575(G;G) individuals, there was no effect of breastfeeding on IQ. *did not replicate those findings. In contrast to their study, (G;G) children exhibited the greatest difference between feeding methods such that breastfed children performed similarly irrespective of child genotype whereas formula fed (G;G) children performed worse than other children on formula milk Breastfeeding ...
common on affy axiom data
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non sig. gwas, hit (p = 5 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
129 snps
(hide) Major histocompatibility complex
1.1x increased risk for schizophrenia
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rs6932590 is a SNP that is postulated to have a role in conferring increased susceptibility for schizophrenia. rs6932590 lies in the major histocompatibility complex (MHC) region on chromosome 6, a region that codes for several genes with significant roles in autoimmunity, such as human leukocyte antigens. Specifically, rs6932590 lies in an intergenic region between PRSS16 (a serine protease expressed in the thymus that plays a role in positive T cell selection) and POM121L2 (a membrane glycoprotein) . The T allele at rs6932590 purportedly confers an increased risk for schizophrenia, with reported odds ratios of 1.16 and 1.31 . === Evidence === One large-scale case-controlled genome-wide association study (GWAS) that examined differential genotypes in individuals with schizophrenia, found ...
1 snp
(hide) Memory
Magnitude: 2
Frequency: 42.5%
Repute:Good
References:11
Frequency: 42.5%
Repute:Good
References:11
increased memory performance
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In a Swiss cohort: 'Carriers of KIBRA rs17070145 T allele had 24% better free recall performance 5 min after word presentation (P = 0.000004) and 19% better free recall performance 24 hours after word presentation (P = 0.0008) than did noncarriers.' In a US cohort: 'T allele carriers had significantly better memory scores than non-carriers in the Buschke's Selective Reminding Test (SRT). Performance on another episodic memory task, the Rey Auditory Verbal Learning Test (AVLT), was also significantly different between allele groups.' In another Swiss cohort, with a visual episodic memory task: 'T allele carriers also performed significantly better than did noncarriers in this population.' 'Functional magnetic resonance imaging detected KIBRA allele-dependent differences in hippocampal activ...
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
1.3x increased risk for alcoholism
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rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism. rs1076560 and the DAT 3'-VNTR variant influences memory Genetic variants altering dopamine D2 receptor expression or function modulate the risk of opiate addiction and the dosage requirements of methadone substitution [PharmGKB:Curated This variant is a potential marker for alcoholism. A allele was more prevalent in the alcoholic patients than in the healthy controls in a study consists of 248 alcohol...
Frequency: 37.2%
References:1
References:1
Frequency: 44.2%
References:2
References:2
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in all 4 ind. samples (1699 total indv.) associated with immediate recall, minor allele (C) carriers displayed worse short-term memory performance in a per allele fashion per HapMap data, the haplotype containing the C allele is in high LD with a (23andMe covered) haplotype consisting of rs4667867(A) (r^2 = 1), rs13421166(C), rs2126152(T), rs6432860(A) (+ the annotated SNP rs3812718(C) ) in the CEU+TSI sample
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rs4790904 is a mutation in the gene encoding PKCα (PRKCA). It has been linked to memory capacity in healthy subjects and to risk for post-traumatic stress disorder .
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. The association between several SNPs in the DTNBP1 gene, most especially rs760761, and schizophrenia was confirmed in a new sample of 1021 cases and 626 controls from Ireland. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and i...
better long-term memory?
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rs1799990, also known as Met129Val or M129V, is a SNP in the prion protein PRNP gene. The more common rs1799990(A) allele encodes the Met (methionine). Historically, since 1991 this SNP has been associated with risk for sporadic Creutzfeldt-Jakob disease, with homozygotes of both types apparently at increased risk compared to heterozygotes. More recently, this SNP has been related to long-term memory with (A;A) and (A;G) individuals recalling 17% more words than (G;G) individuals at 24h following learning. A further study of 12 individuals of each of the 3 possible genotypes showed that at both 30 minutes and 24 hour time lags, correlations between retrieval-related brain activity and retrieval success were negative for (G;) homozygotes (the more activity, the worse retrieval success), whi...
(hide)
g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
(hide)
g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
13 snps
(hide) Menopause
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23andMe blog rs1172822(T) Menopause about 25 weeks earlier [OMIM:?] [GWAS:Menopause]
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rs4806660 is a SNP on chromosome 19. A case control study of ~2,000 women found that each rs4806660(C) allele was associated with an average decrease in age at menopause of ~1 month. This also meant that each rs4806660(T) allele yielded an odds ratio of 1.45 (CI: 1.32–1.59, p = 8.88 x 10e-16) of not having early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low. [OMIM:?]
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23andMe blog rs365132(T) Menopause about 20 weeks later [OMIM:?] [GWAS:Menarche and menopause (age at onset)]
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rs9379896 is a SNP on chromosome 6. A case control study of ~2,000 women found that each rs9379896(C) allele was associated with an average increase in age at menopause of ~1 month. This also meant that each rs9379896(T) allele yielded an odds ratio of 1.13 (CI: 1.01–1.27, p = 3.8 x 10e-2) of early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low.
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[GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
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23andMe blog rs2153157(A) Menopause about 15 weeks later [OMIM:MENOPAUSE, NATURAL, AGE AT, QUANTITATIVE TRAIT LOCUS 1; MENOQ1] [GWAS:Menarche and menopause (age at onset)]
Frequency: 60.4%
References:1
References:1
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[GWAS:Menopause]
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[OMIM:?] [GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
common on affy axiom data
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23andMe blog rs7333181(A) Menopause about 27 weeks later [OMIM:MENOPAUSE, NATURAL, AGE AT, QUANTITATIVE TRAIT LOCUS 1; MENOQ1] [GWAS:Menopause]
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:1
Frequency: 76.1%
Repute:Good
References:1
Magnitude: 0
Frequency: 82.3%
Repute:Good
References:9
Frequency: 82.3%
Repute:Good
References:9
common on affy axiom data
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rs16991615 is a nonsynonymous SNP on chromosome 20. A case control study of ~2,000 women found that each rs16991615(A) allele was associated with an average increase in age at menopause of 11 months. This also meant that each rs16991615(G) allele yielded an odds ratio of 1.85 (CI: 1.51–2.2, p = 1.45 x 10e-9) of early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low. * see also 23andMe blog [OMIM:?] [GWAS:Menarche and menopause (age at onset)]
17 snps
(hide) Mental health
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rs4675690 is in close proximity to CREB1, and adjacent to LOC151194. g2b2mh blog individuals with the TT genotype at rs4675690 (C/T) showed less disgust, but not happiness, desire or fear. T allele associated with increased chance of suicide (OR = 2.3, 95% CI 1.3-2.9, TT homozygotes vs CC homozygotes?) during the first 30 days (p > 0.05 after the first month) of citalopram treatment, in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males...
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g2b2mh blog rs833070 and rs2146323. Individuals with the CC genotype at rs833070 and rs2146323 displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively.
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origins associated with an independent aspect of decision making in a learning paradigm Association analysis of the protein phosphatase 1 regulatory subunit 1B (PPP1R1B) gene with nicotine dependence in European- and African-American smokers. Genetic analysis of the gene coding for DARPP-32 (PPP1R1B) in Japanese patients with schizophrenia or bipolar disorder. Reduced prefrontal cortex DARPP-32 mRNA in completed suicide victims with schizophrenia. The biological basis of anger: associations with the gene coding for DARPP-32 (PPP1R1B) and with amygdala volume. Dopaminergic genes predict individual differences in susceptibility to confirmation bias. Variation of the gene coding for DARPP-32 (PPP1R1B) and brain connectivity during associative emotional learning.
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associated with vulnerability to nicotine addiction in men. g2b2mh blog rs1044396 mediates effects of nicotine self-medication via parietal cortex. subjects with the (T;T) genotype showed robust brain activity in the parietal cortex while subjects with the (C;C) genotype showed very little change in activity. [PharmGKB:Curated This variant is closely linked to rs2236196 and has been associated with the intensification of nicotine dependence.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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origins blog linked to brain mophology via a haplotype block with rs833070 and rs2146323, Large-scale evaluation of candidate genes identifies associations between VEGF polymorphisms and bladder cancer risk. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Polymorphisms in the VEGFA and VEGFR-2 genes and neovascular age-related macular degeneration. Vascular endothelial growth factor gene polymorphisms and ovarian cancer survival. Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms. Contribution of VEGF polymorphisms to variation in VEGF serum levels in a healthy population.
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origins blog rs833070 and rs2146323. Individuals with the CC genotype at rs833070 and rs2146323 displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively. bdmh2 blog coverage of rs833070 and rs2146323
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. The association between several SNPs in the DTNBP1 gene, most especially rs760761, and schizophrenia was confirmed in a new sample of 1021 cases and 626 controls from Ireland. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and i...
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
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asthma related influences sleep patterns [http://originsgenomeresources.net/musings/?p=62] [OMIM:ASTHMA SUSCEPTIBILITY 2]
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
common in complete genomics
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rs964201 is an A/G SNP located in the ASPM gene. The G-allele of this SNP as well as the A-allele of rs3762271 another SNP located in the ASPM gene and rs2442496 a SNP in the MCPH1 gene arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans. A comment is found at g2b2mh.
common in complete genomics
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origins associated with an independent aspect of decision making in a learning paradigm
13 snps
(hide) Micronutrient Metabolism
Frequency: 50.8%
References:49
References:49
increased type-2 diabetes risk; higher gestational diabetes risk
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rs10830963 was associated with an increased risk of type-2 diabetes in our Han Chinese cohort (OR 1.16, 95% CI 1.03-1.31, p = 0.015). As previously described, the risk variant was also associated with increased fasting plasma glucose, showing an increase of 0.068 mmol/l (95% CI 0.036-0.100, p = 4 x 10(-5)) per risk allele rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations and reduced OGTT- and IVGTT-induced insulin release. rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release A study totaling 19,000+ Europeans concluded that rs10830963 had the most influence of any MTNR1B gene SNP on the risk for type-2 diabetes. Specifically, the (G) allele increase...
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Association of a common nonsynonymous variant in GLUT9 with serum uric acid levels in old order amish.
6 snps
(hide) MicroRNA
Magnitude: 3
Frequency: 33.6%
Repute:Bad
References:35
Frequency: 33.6%
Repute:Bad
References:35
increased risk of various types of cancer This variant increases risk of numerous types of cancer in many studies. It is in a microRNA
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miRNA sequences and non-small cell lung cancer rs11614913 SNP in hsa-mir-196a2 was associated with survival in individuals with NSCLC. Specifically, survival was significantly decreased in individuals who were homozygous CC at SNP rs11614913. microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs11614913 in hsa-mir-196a2 T>C 1.23; 95% confidence interval [CI], 1.02-1.48 *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Signatures of purifying and local positive selection in human miRNAs. MicroRNA polymorphisms: the future of pharmacogenomics...
decreased cancer risk source
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microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Genetic variants of miRNA sequences and non-small cell lung cancer survival. MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. SNPs in human miRNA genes affect biogenesis and function. Common genetic variants in pre-microRNAs are associated with risk of coal workers' pneumoconiosis. MicroRNA polymorphisms: a giant leap towards personalized medicine. Common genetic variants in pre-microRNAs and risk of gallbladder cancer in North Indian population. Association of pre-microRNAs genetic varia...
0.58x decreased risk for esophageal cancer
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rs6505162 is a SNP located in the pre-miRNA region of mir423. The major allele is rs6505162(C). A study of 346 Caucasians with esophageal cancer found that compared with the homozygous wild-type genotype of rs6505162, individuals with the heterozygous and homozygous variant genotype had a significantly reduced esophageal cancer risk with odds ratios of 0.58 (CI: 0.41-0.82) and 0.43 (CI: 0.27-0.68), respectively. After stratifying by gender, smoking, and age, the authors discovered that the protective effect was significant only for individuals under 64 years of age, regardless of sex or whether they smoked. Other unfavorable genotypes (ie SNPs) were also identified that were not as significant as rs6505162, and the overall risk of esophageal cancer increased with increasing numbers of unfa...
Frequency: 13.6%
References:1
References:1
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Association of the tag SNPs in the human SKT gene (KIAA1217) with lumbar disc herniation. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
2x higher ER- breast cancer risk
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microRNA 749 Swedish incident breast cancer cases with detailed clinical data and up to 15 years of follow-up together with 1493 matched controls. The strongest association was between the rs743554(T) allele of the ITGB4 gene and estrogen receptor negative (ER-) tumors (odds ratio 2.09, CI: 1.19-3.67) and worse survival compared to the wild type genotype carriers (hazard ratio [HR] 2.11, CI: 1.21-3.68). The poor survival was significantly associated with the aggressive tumour characteristics: high grade, lymph node metastasis and high stage.
Frequency: 26.5%
References:0
References:0
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973, the C allele of rs1811399, and the C allele of rs1234747 may contribute to autism by affecting microRNA
Frequency: 36.3%
References:1
References:1
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Tissue effect on genetic control of transcript isoform variation. Fine-scale variation and genetic determinants of alternative splicing across individuals.
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
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discussed in nature Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Genetic Polymorphisms in MicroRNA-Related Genes as Predictors of Clinical Outcomes in Colorectal Adenocarcinoma Patients.
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973, the C allele of rs1811399, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:1
Frequency: 85.8%
Repute:Good
References:1
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seems to have a microrna snp near 8q24 rs10109700 rs7832031 Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.
Magnitude: 0
Frequency: 90.0%
Repute:Good
References:1
Frequency: 90.0%
Repute:Good
References:1
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seems to have a microrna snp near 8q24 rs10109700 rs7832031
Magnitude: 0
Frequency: 93.7%
Repute:Good
References:0
Frequency: 93.7%
Repute:Good
References:0
Magnitude: 0
Frequency: 96.9%
Repute:Good
References:0
Frequency: 96.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 98.5%
Repute:Good
References:1
Frequency: 98.5%
Repute:Good
References:1
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
References:1
Frequency: 100.0%
References:1
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
common in complete genomics
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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endothelial dysfunction seen in hypertensive subjects. notable that the authors initiated their own dbsnp entry and cite the ss# in the abstract as well as relating to microRNA
normal
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(C;C) predisposes to papillary thyroid carcinoma. Among 42 patients with familial breast cancer and 82 patients with ovarian cancer, those with at least one rs2910164(C) SNP tended to have been diagnosed at an earlier age than those with only (G) alleles. For the breast cancer patients, the difference in median age was between 45 vs 56 (p = 0.029) and for ovarian cancer patients, 45 vs 50, (p = 0.014). (G;G) males were two-fold more susceptible to hepatocellular carcinoma (OR = 2.016, 95% CI = 1.056-3.848, P = 0.034) perhaps an ambiguous flip? [OMIM:MICRO RNA 146A; MIRN146A]
57 snps
(hide) Mitochondrial Haplogroup
Frequency: 0.0%
References:0
References:0
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haplogroups
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haplogroups
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haplogroups
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haplogroups ,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=G |derived_allele=A }}
Frequency: 100.0%
References:0
References:0
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haplogroups
References:0
References:0
References:0
References:0
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haplogroups
References:1
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|tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2b |ancestral_allele=T |derived_allele=C }}
common on affy axiom data
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haplogroups ,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=T |derived_allele=C }}
common on affy axiom data
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haplogroups ,,Shen 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H1 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Frequency: 85.9%
References:1
Frequency: 85.9%
References:1
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:0
Frequency: 88.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 89.1%
References:0
Frequency: 89.1%
References:0
Magnitude: 0
Frequency: 89.2%
References:0
Frequency: 89.2%
References:0
Magnitude: 0
Frequency: 89.2%
Repute:Good
References:0
Frequency: 89.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 90.8%
References:0
Frequency: 90.8%
References:0
Magnitude: 0
Frequency: 92.3%
References:0
Frequency: 92.3%
References:0
Magnitude: 0
Frequency: 95.3%
References:0
Frequency: 95.3%
References:0
common on affy axiom data
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haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H2 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Frequency: 95.4%
References:0
Frequency: 95.4%
References:0
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haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2a |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Frequency: 96.8%
References:0
Frequency: 96.8%
References:0
Magnitude: 0
Frequency: 96.9%
References:0
Frequency: 96.9%
References:0
Magnitude: 0
Frequency: 96.9%
References:0
Frequency: 96.9%
References:0
common on affy axiom data
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Two novel pathogenic mitochondrial DNA mutations affecting organelle number and protein synthesis. Is the tRNA(Leu(UUR)) gene an etiologic hot spot? Mutational analysis of the mitochondrial 12S rRNA gene in Chinese pediatric subjects with aminoglycoside-induced and non-syndromic hearing loss. The role of selection in the evolution of human mitochondrial genomes.
Magnitude: 0
Frequency: 100.0%
References:0
Frequency: 100.0%
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
References:0
Frequency: 100.0%
References:0
Magnitude: 0
Frequency: 100.0%
References:0
Frequency: 100.0%
References:0
Magnitude: 0
Frequency: 100.0%
References:0
Frequency: 100.0%
References:0
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haplogroups
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haplogroups
Magnitude: 0
References:0
References:0
Magnitude: 0
References:0
References:0
Magnitude: 0
References:0
References:0
common on affy axiom data
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haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a2 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
References:1
References:1
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|tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1 |derived_haplogroup=H1c |ancestral_allele=T |derived_allele=C }}
Magnitude: 0
References:1
References:1
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haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1 |derived_haplogroup=H1a |ancestral_allele=A |derived_allele=G }}
Magnitude: 0
References:0
References:0
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haplogroups
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haplogroups
77 snps
(hide) NAT2
Magnitude: 1.7
Most non-Scandinavian Caucasians and approximately half of African-Americans are slow metabolizers. This variation is important because of its primary role in the deactivation of many chemicals in the body's environment, including those produced by caffeine and cigarettes as well as aromatic amine and hydrazine drugs used medicinally. In general, slow metabolizers have higher rates of certain types of cancer and are more susceptible to side effects from chemicals metabolized by NAT2. According to this source 6 snps determine NAT2 metabolism. The way their genotypes interact is very complex, which makes this one of the largest genosets in SNPedia. The SNPs are: *rs1208 *rs1041983 *rs1799929 *rs1799930 *rs1799931 *rs1801280
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
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rs1041983 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1041983(T). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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rs1799929 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799929(T). When this SNP is indicative of carrying a NAT2*5A allele, the following may be relevant: A study (based on only 42 patients) found that women with the NAT2*5A slow genotype (which presumably means rs1799929(T;T)) had a significantly higher risk of cervical cancer compared with individuals with the NAT2*5A fast genotype (i.e. carriers of only one rs1799929(T) allele), with a reported odds ratio of 7.469 (CI: 1.6-33.3, p=0.008). [PharmGKB:Curated in vitro study; PK: 20-fold reduction...
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rs1801280 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801280(C). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
common in complete genomics
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With 99% sensitivity and 95% specificity, rs1495741 is reported to classify the NAT2 phenotype of an individual; it therefore is a candidate to replace the 7-SNP panel used in genosets such as gs138, gs139, and gs140. [GWAS:None]
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
common in complete genomics common for Caucasians on the 23andme platform
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rs1801279 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801279(A). [PharmGKB:Curated Homozygous A allele is slow acetylator phenotype (altered rates of metabolism of arylamines). May be associated with higher risk for bladder cancer and lower risk for colorectal cancer.]
common in complete genomics
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[PharmGKB:Curated Homozygous A allele is slow acetylator phenotype.]
1 genoset 11 snps
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Magnitude: 2
Frequency: 55.8%
Repute:Bad
References:1
Frequency: 55.8%
Repute:Bad
References:1
very common, but higher risk of Parkinson's disease approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease. It is notable because it is the first snp patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
more likely to go bald more likely to go bald
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Along with rs201571 serves as a proxy for rs1160312. related to baldness
3x increased testicular cancer risk for men
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Testicular germ cell tumor risk I('TGCT'; i.e. testicular cancer risk) was increased 40% per copy of the major allele (C) at rs4324715 and rs6897876 (OR = 1.37, CI: 1.14–1.64; OR = 1.39, CI: 1.16–1.66, respectively), based on a genome-wide scan of 277 primarily Caucasian TGCT cases and 919 controls. Men who have two copies of the common version of the sprouty 4 SPRY4 gene have a 1.5-fold higher risk of testicular cancer than men who have two copies of the less common or minor version of the gene. [doi|10.1038/ng.393]
Frequency: 0.0%
References:1
References:1
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[GWAS:None]
Frequency: 0.9%
References:2
References:2
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[GWAS:None]
Frequency: 0.9%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 1.8%
References:1
References:1
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[GWAS:None]
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mentioned as potentially affecting grey matter volume, sample size tiny
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[GWAS:None]
Frequency: 3.5%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
Frequency: 6.2%
References:1
References:1
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[GWAS:None]
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: T, MAF= 0.40, combined P value= 5.62E-04.]
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[GWAS:None]
Frequency: 7.9%
References:2
References:2
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[GWAS:None]
Frequency: 8.0%
References:1
References:1
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[GWAS:None]
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Tooth Development [GWAS:None]
Frequency: 9.2%
References:1
References:1
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Cytokine SNPs: Comparison of allele frequencies by race and implications for future studies.
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[GWAS:None]
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[GWAS:None]
Frequency: 12.5%
References:1
References:1
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[GWAS:None]
Frequency: 14.2%
References:1
References:1
Frequency: 14.2%
References:1
References:1
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rs10494366, rs4657139 and rs16847548 were significantly associated with adjusted QT interval in whites. relative hazard of SCD associated with each C allele at rs16847548 was 1.31. rs12567209 was also independently associated with SCD in whites (relative hazard 0.57, 95% confidence interval 0.39 to 0.83, P=0.003). No significant associations observed in blacks. Multiple independent genetic factors at NOS1AP modulate the QT interval in a multi-ethnic population. Genetic variation in NOS1AP is associated with sudden cardiac death: evidence from the Rotterdam Study.
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[GWAS:None]
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Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33.
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mentioned by gs240
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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Gene-environment interaction effects on the development of immune responses in the 1st year of life. Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data. A functional SNP of interferon-gamma gene is important for interferon-alpha-induced and spontaneous recovery from hepatitis C virus infection. Interferon gamma allelic variants: sex-biased multiple sclerosis susceptibility and gene expression. Host genetic factors and vaccine-induced immunity to hepatitis B virus infection. A single nucleotide polymorphism (A --> G) in intron 3 of IFNgamma gene is associated with asthma. Host genetic factors and vaccine-induced immunity to HBV infection: haplotype analysis. IFNG genotype and sex interact to influence the risk of chi...
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[GWAS:None]
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[PharmGKB:Curated in a GWAS of subjects of African ancestry(African American plus African Caribbean), this SNP was found to be significantly associated with Asthma . This finding was not significantly replicated in 4 additional case-control studies of African Americans nor in tested family and case-control panels of UK and German subjects. Risk or phenotype-associated allele: A. Phenotype: increased risk for asthma. Study size/population/ethnicity: 1) 935 African American asthmatic cases and control subjects from the Baltimore-Washington area (2) 929 African Caribbean asthmatic subjects and their family members from Barbados . Significance metric(s): combined p = 3.05 x 10(-6); OR = 0.65(95% CI= 0.49 -0.87). Type of association: CO; GN.]
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[GWAS:None]
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Associated with bipolar disorder in individuals of European ancestry. [GWAS:Bipolar disorder and schizophrenia]
Frequency: 19.5%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 20.4%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
0.74x decreased risk for Non-hodgkin's lymphoma
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rs4833103 is a SNP located in a cluster of toll-like receptor genes. In a pooled analysis including three population-based case-control studies of Non-Hodgkin's lymphoma (1,946 cases, 1,808 controls), two SNPs in moderate linkage disequilibrium were significantly associated with NHL: rs10008492 (odds ratio for (C;T) genotype 1.12, CI: 0.97-1.30; OR(T;T) 1.40, CI: 1.15-1.71; p(trend)=0.001) and rs4833103 (OR(A;C) 0.75, CI: 0.64-0.88; OR(A;A) 0.74, CI: 0.62-0.90; p(trend)=0.002; p(dominant)=0.0002).
Frequency: 22.1%
References:2
References:2
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Association between liver X receptor alpha gene polymorphisms and risk of metabolic syndrome in French populations. Functional and genetic analysis in type 2 diabetes of liver X receptor alleles--a cohort study. Genetic variation within the NR1H2 gene encoding liver X receptor beta associates with insulin secretion in subjects at increased risk for type 2 diabetes. Associations between common genetic polymorphisms in the liver X receptor alpha and its target genes with the serum HDL-cholesterol concentration in adolescents of the HELENA Study. Liver X receptor alpha gene polymorphisms and variable cardiovascular outcomes in patients treated with antihypertensive therapy: results from the INVEST-GENES study.
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[GWAS:None]
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[GWAS:None]
Frequency: 23.9%
References:2
References:2
Frequency: 23.9%
References:1
References:1
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[GWAS:None]
Frequency: 23.9%
References:1
References:1
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[GWAS:None]
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
Frequency: 24.8%
References:1
References:1
Frequency: 24.8%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
Frequency: 26.5%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. In combination, rs10018204, rs11222869, rs16965867, rs1846644, and rs6539870 were significant predictors of etoposide IC50, accounting for 55% of the etoposide IC50 variation in Caucasians. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00009. Type of association: FA; GN.]
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Genomewide association study for susceptibility genes contributing to familial Parkinson disease.
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[GWAS:None]
1.5x increased risk for meningioma
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rs4968451, which is in a breast cancer susceptibility gene, was associated with increased risk of meningioma, a common form of brain tumor, in a combination of five studies totaling 631 European patients. The odds ratio was 1.57 (CI: 1.28-1.93, p=.009 after adjusting for multiple testing) for the risk allele, rs4988451(C). Around 30% of Europeans carry one of risk genotypes, i.e. rs4968451(A;C) or (C;C); and perhaps 16% of meningiomas might be associated with this SNP.
Frequency: 27.4%
References:1
References:1
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
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[GWAS:None]
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associated with specific patterns of brain activity. rs3087454 rs1355920 rs7520974 rs885834
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[GWAS:None]
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
Frequency: 31.5%
References:2
References:2
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[GWAS:None]
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Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms. [GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 32.1%
References:1
References:1
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[GWAS:None]
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Gene-nutrient interactions among determinants of folate and one-carbon metabolism on the risk of non-Hodgkin lymphoma: NCI-SEER case-control study.
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[GWAS:None]
Frequency: 33.6%
References:1
References:1
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rs1741981 and rs2547547 influence risk for postoperative hepatocellular carcinoma tumor recurrence up to 2.2x Detection of fetomaternal genotype associations in early-onset disorders: evaluation of different methods and their application to childhood leukemia.
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This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs7582658, was deemed to be the core SNP of a region on chromosome 2 with 274 SNPs spanning 2282KB from 2:188489676 to 2:190772106 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as...
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
Frequency: 35.4%
References:1
References:1
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
Frequency: 35.4%
References:1
References:1
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[GWAS:None]
Frequency: 35.4%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:Colorectal cancer]
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[GWAS:None]
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rs231725 associated with primary biliary cirrhosis
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[GWAS:None]
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the rs1411766 locus may be commonly involved in conferring susceptibility to diabetic nephropathy among subjects with type 1 or type 2 diabetes across different ethnic groups.
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[GWAS:None]
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Baldness paper from 23andMe June 2012 [GWAS:None]
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Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. [GWAS:None]
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[GWAS:None]
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
Frequency: 38.1%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
Frequency: 38.4%
References:4
References:4
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Association of Toll-like receptor 4 gene polymorphisms with normal tension glaucoma. Association analysis of Toll-like receptor 4 polymorphisms with autoimmune pancreatitis. Lack of association between toll-like receptor 4 gene polymorphisms and sarcoidosis-related uveitis in Japan. Traffic-related air pollution, oxidative stress genes, and asthma (ECHRS). Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies.
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 89. Study population/ethnicity: 89 Yorubans. Significance metric(s): p = 0.00003. Type of association: FA; GN.]
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[GWAS:None]
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[GWAS:None]
Frequency: 38.9%
References:0
References:0
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[GWAS:None]
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[PharmGKB:Curated This variant is associated with hip fracture in a GWAS study consisting of 403 chinese females (266 with hip fracture and 177 control subjects).]
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rs2631372 increases susceptibility to Crohn's disease 1.28 times for carriers of the C allele
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 40.2%
References:4
References:4
1.19x increased risk for T2D
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rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP. type-2 diabetes rs2297508(C) and rs11868035(C) This SNP rs11868035 and rs1057217 are associated with increased risk of schizophrenia in German and Scandinavian samples. This SNP and rs6812193 are reported to affect risk of Parkinson's disease. plos Polymorphisms in the gene encoding sterol regulatory element-binding factor-1c are associated with type 2 diabetes. [PharmGKB:Curated This SNP in the SREBF1 gene was strongly associated with schizophrenia in German, Danish and Norwegian samp...
Frequency: 40.7%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00007691; OR for minor allele A:1.256)]
Frequency: 40.7%
References:3
References:3
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Chromosome 15q25.1 genetic markers associated with level of response to alcohol in humans.
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[GWAS:None]
normal
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A very small study of 117 healthy European peri- and postmenarcheal girls (14.9 +/- 1.6 years) were followed for 4 years along with their calcium intake. Girls with rs4516035(C;T) and (C;C) genotypes had 13% lower spine mineral content if their milk intakes were below 260 mL/day, compared to either genotype-matched girls with higher milk intakes or to girls with the (T;T) genotype. If this is real, it suggests that rs4516035(C;T) and (C;C) female teens need more milk than rs4516035(T;T) girls to have optimal bone density. rs4516035 and the more aggressive tumour location in head-neck and trunk (OR=1.54, p=0.020)
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ADHD GIT1 is associated with ADHD in humans and ADHD-like behaviors in mice
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[GWAS:None]
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[GWAS:None]
Frequency: 41.5%
References:1
References:1
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[GWAS:None]
Frequency: 41.6%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 42.5%
References:1
References:1
Frequency: 42.5%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00004278; OR for minor allele C:1.255)]
1.3x increased risk for Crohn's disease with ileal involvement
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rs3814570 is a SNP in the transcription factor 7-like 2 (T-cell specific, HMG-box) TCF7L2 gene. A study of 784 Crohn's disease patients with ileal involvement concluded that rs3814570 was associated with increased risk, but not with risk for colonic Crohn's disease or ulcerative colitis. The odds ratio was 1.27 (CI: 1.07 - 1.52, p = 0.00737). Evidence for association between polycystic ovary syndrome (PCOS) and TCF7L2 and glucose intolerance in women with PCOS and TCF7L2.
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[GWAS:None]
Frequency: 42.9%
References:1
References:1
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[GWAS:None]
Frequency: 43.4%
References:1
References:1
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[GWAS:None]
Frequency: 43.8%
References:1
References:1
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[GWAS:None]
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[GWAS:Height]
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[GWAS:None]
Frequency: 44.2%
References:3
References:3
Frequency: 44.2%
References:0
References:0
Frequency: 44.2%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
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rs4693596(C;C) 2x odds of myopathy when taking statins. Statin Response
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00007324; OR for minor allele A:0.804)]
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[GWAS:None]
Frequency: 46.0%
References:1
References:1
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[GWAS:None]
Frequency: 46.0%
References:1
References:1
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[GWAS:None]
1.4x increased gastric cancer risk. Increased risk of Acute Graft-Versus-Host Disease after Unrelated Bone Marrow Transplantation
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rs2275913, also known as G-197A, is a SNP in the IL17A gene. A study of 811 Japanese subjects (524 without gastric cancer and 287 with gastric cancer) reported an odds ratio of 1.42 (CI: 1.09-1.85, p=0.01) for the rs2275913(A) allele, and 3.02 (CI: 1.86-4.91, p<0.0001) for the (A;A) genotype, with gastric cancer. This 'A'-allele of this SNP is also functionally associated with acute Graft-Versus-Host Disease after unrelated bone marrow transplantation
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[GWAS:Cognitive performance]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00007. Type of association: FA; GN.]
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[GWAS:None]
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[GWAS:None]
Frequency: 46.4%
References:1
References:1
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The enabled homolog gene polymorphisms are associated with susceptibility and progression of childhood IgA nephropathy.
Frequency: 46.4%
References:1
References:1
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[GWAS:None]
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.0000151;OR for minor allele C:0.785).]
Frequency: 46.8%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00006. Type of association: FA; GN.]
Frequency: 46.9%
References:0
References:0
Frequency: 46.9%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated This SNP on 5p14.1 was associated with autism spectrum disorder in a combined analysis of four GWAS data sets with a total of more than 10,000 subjects of European ancestry. This SNP is in an intergenic region between CDH10 and CDH9 that contains several highly conserved genomic elements.]
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00009. Type of association: FA; GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: This SNP was associated with a greater reduction in total cholesterol after at least 1 week of statin use. This was not replicated in a second cohort. Study size: 546 (original cohort); 100 (replication cohort). Study population/ethnicity: People taking statins; age 55 or older; Rotterdam Study; Netherlands. Significance metric(s): p = 0.05 (original); p = 0.975 (replication) Type of association: PD.]
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[GWAS:None]
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[GWAS:None]
Frequency: 48.2%
References:1
References:1
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[GWAS:None]
Frequency: 48.7%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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finds no association between rs11832 and pulmonary emphysema
Frequency: 49.6%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
Frequency: 50.4%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.000004333; OR for minor allele T:0.786)]
Frequency: 50.4%
References:2
References:2
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(C;C) greater odds of longevity Replication of an association of variation in the FOXO3A gene with human longevity using both case-control and longitudinal data. Association of the FOXO3A locus with extreme longevity in a southern Italian centenarian study.
Frequency: 51.3%
References:1
References:1
Frequency: 51.3%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.00008365;OR for minor allele G:1.212).]
Frequency: 51.3%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: Decreased fasting insulin. Study size: 4681. Study population/ethnicity: Replication study of Swedish control subjects. Significance metric(s): p = 0.001. Type of association: FA; GN.]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.00003; OR: 5.5 (1.8, 20.2)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia.
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 53.8%
References:0
References:0
Frequency: 54.0%
References:1
References:1
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[GWAS:None]
Frequency: 54.9%
References:0
References:0
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23andMe blog blood pressure
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[GWAS:None]
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[GWAS:None]
Frequency: 56.6%
References:1
References:1
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
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[GWAS:None]
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[GWAS:None]
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? T allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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association with restless leg syndrome
Frequency: 60.2%
References:2
References:2
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[GWAS:None]
Frequency: 62.8%
References:1
References:1
Frequency: 62.8%
References:1
References:1
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[GWAS:None]
Frequency: 63.3%
References:1
References:1
somewhat higher risk for prostate cancer
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rs13149290 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=2.5 x 10e-5, using a dominant model of risk.
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
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[GWAS:None]
Frequency: 64.6%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 66.4%
References:1
References:1
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23andMe blog multiple sclerosis rs17066096 IL22RA2 G 1.14 [GWAS:None]
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A second-generation genomewide screen for asthma-susceptibility alleles in a founder population. [GWAS:None]
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[GWAS:None]
Frequency: 66.7%
References:1
References:1
Frequency: 67.3%
References:1
References:1
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[GWAS:None]
Frequency: 69.0%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 69.6%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 69.9%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 72.6%
References:1
References:1
Frequency: 72.6%
References:1
References:1
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[GWAS:None]
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Elevated expression and genetic association links the SOCS3 gene to atopic dermatitis. Elevated expression and polymorphisms of SOCS3 influence patient response to antiviral therapy in chronic hepatitis C. Lack of association between the tagging SNP A+930-->G of SOCS3 and type 2 diabetes mellitus: meta-analysis of four independent study populations. Gene expression and hepatitis C virus infection. Polymorphisms near SOCS3 are associated with obesity and glucose homeostasis traits in Hispanic Americans from the Insulin Resistance Atherosclerosis Family Study.
Frequency: 73.5%
References:1
References:1
Frequency: 75.2%
References:1
References:1
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[GWAS:None]
Frequency: 75.9%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 76.1%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 76.1%
References:1
References:1
Frequency: 76.1%
References:2
References:2
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 78.0%
References:1
References:1
(hide)
[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: A, MAF= 0.15, combined P value= 4.89E-05. It is also associated with etoposide clearance.]
Frequency: 78.8%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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Population substructure and control selection in genome-wide association studies.
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 83.2%
References:1
References:1
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[GWAS:None]
Frequency: 84.1%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.00005649;OR for minor allele T:1.504).]
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[GWAS:None]
Frequency: 85.8%
References:1
References:1
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[GWAS:None]
Frequency: 85.8%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 88.5%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:Cognitive performance]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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Association study of mast cell chymase polymorphisms with atopy. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. Power of multifactor dimensionality reduction and penalized logistic regression for detecting gene-gene interaction in a case-control study. Impact of polymorphisms of the genes encoding angiotensin II-forming enzymes on the progression of IgA nephropathy.
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discussed in nature Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Genetic Polymorphisms in MicroRNA-Related Genes as Predictors of Clinical Outcomes in Colorectal Adenocarcinoma Patients.
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Variants of CTGF are associated with hepatic fibrosis in Chinese, Sudanese, and Brazilians infected with schistosomes.
Magnitude: 0
Frequency: 45.1%
References:1
Frequency: 45.1%
References:1
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G-C-T-C haplotype of rs2340690-rs788016-rs2305560-rs2565163 has odds ratio of 1.91 (CI: 1.26-2.89, p=0.002) for coronary heart disease compared to G-T-T-C, based on a study of 1,000 Han Chinese patients and matched controls. * Note: Haplotype allele assignments may not be in dbSNP orientation.
Magnitude: 0
Frequency: 46.9%
Repute:Good
References:1
Frequency: 46.9%
Repute:Good
References:1
Magnitude: 0
Frequency: 75.0%
References:0
Frequency: 75.0%
References:0
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A GCH1 Haplotype Associated with Susceptibility to Vasoocclusive Pain and Impaired Vascular Function in Sickle Cell Anemia
Magnitude: 0
Frequency: 80.5%
Repute:Good
References:0
Frequency: 80.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:2
Frequency: 85.0%
Repute:Good
References:2
normal
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rs10754339 is a SNP in the V-set domain containing T cell activation inhibitor 1 VTCN1 gene, which is also known as B7-H4. A study of 500 Chinese Han women with breast cancer (and an equal number of matched controls) concluded that the rs10754339(A;G) genotype and G allele showed a significantly increased risk of breast cancer (odds ratio 1.455, CI: 1.119-1.892, and 1.325, CI: 1.073-1.637, respectively). Additionally, the rs10754339(G;G) genotype was significantly associated with lymph node metastasis and PR status, and the G allele and the (A;G) genotype were respectively associated with lymph node metastasis and ER status.
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:1
Frequency: 85.8%
Repute:Good
References:1
Magnitude: 0
Frequency: 87.2%
Repute:Good
References:0
Frequency: 87.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:1
Frequency: 90.3%
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: A, MAF= 0.06, combined P value= 2.63E-05.]
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:0
Frequency: 90.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 90.6%
Repute:Good
References:3
Frequency: 90.6%
Repute:Good
References:3
common in complete genomics
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rs12467557 increases susceptibility to Substance dependence, Nicotine 1.81 times for carriers of the C allele
Magnitude: 0
Frequency: 90.9%
Repute:Good
References:1
Frequency: 90.9%
Repute:Good
References:1
normal
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rs6013029 is a SNP in the CTNNBL1 gene. Found no evidence of early onset obesity or increased body mass index association with this SNP in several populations (~3,000 cases overall) of Central European (German) ancestry. While the older a study of ~1,900 Caucasians turned up associations between several SNPs in the CTNNBL1 gene and increased risk for obesity, of which rs6013029 was statistically the strongest, with an odds ratio of 1.42 for (T;T) homozgyotes compared to (G;G) homozygotes. This SNP achieved experiment-wise p values of 2.69 x 10<sup>-7</sup> for body mass index (BMI) and of 4.99 x 10<sup>-8</sup> for fat mass, respectively. The rs6013029(T) allele confers an average increase in BMI and fat mass of 2.67 kg/m(2) and 5.96 kg, respectively, compared to rs...
Magnitude: 0
Frequency: 96.5%
Repute:Good
References:1
Frequency: 96.5%
Repute:Good
References:1
Magnitude: 0
Frequency: 97.3%
Repute:Good
References:0
Frequency: 97.3%
Repute:Good
References:0
common in complete genomics
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[PharmGKB:Curated Based on an study on 284 Mexican Americans, this variant in the 5' UTR of PSMB4 is significantly associated with major depressive disorder (MDD). The results implicate that the specific UTR variation increases the risks for a T-cell dysfunction in MDD in the studied population.]
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The association of single nucleotide polymorphisms in the 5'-regulatory region of the lumican gene with susceptibility to high myopia in Taiwan. High myopia is not associated with the SNPs in the TGIF, lumican, TGFB1, and HGF genes. The association of haplotype at the lumican gene with high myopia susceptibility in Taiwanese patients. Association of lumican gene with susceptibility to pathological myopia in the northern han ethnic chinese.
common in complete genomics
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chronic lymphocytic leukemia rs2266690 rs17028658 rs4505265 rs1045485 rs2779251 rs3136687
common in complete genomics
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: G, MAF= 0.04, combined P value= 3.73E-04.]
458 snps
(hide) Native American
Duffy-positive This genotype is associated with European populations and southwestern Native American populations.
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rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. (One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.) Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and southwestern Native American populations. rs2814778(G;G) protect against Plasmodium vivax malaria and predicts of white blood cell and neutrophil count 23andMe blog discussion Malaria Resistance (Duffy Antigen) [PharmGKB:Curated A...
common one paper reports increased risk of alcoholism for African-Americans with this genotype.
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This paper found significant association with rs2066702, the SNP that defines ADH1B*3, in African American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B*1, and the low-risk allele encodes ADH1B*3. A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.In some African American] and Native American populations, the ADH1B*3 allele (Arg369Cys in exon 9) is correlated with protection against alcoholism. [PharmGKB:In-Depth This allele has been found in some African American and Native American populations to be correlated with prote...
2 snps
(hide) Neanderthal
Frequency: 12.4%
References:0
References:0
Frequency: 31.9%
References:0
References:0
Frequency: 38.9%
References:0
References:0
Frequency: 41.6%
References:1
References:1
Frequency: 44.2%
References:0
References:0
Frequency: 46.4%
References:1
References:1
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The enabled homolog gene polymorphisms are associated with susceptibility and progression of childhood IgA nephropathy.
Frequency: 64.6%
References:0
References:0
Frequency: 73.5%
References:0
References:0
Frequency: 77.7%
References:0
References:0
Frequency: 77.9%
References:0
References:0
Frequency: 77.9%
References:0
References:0
Frequency: 77.9%
References:0
References:0
Frequency: 78.5%
References:0
References:0
Frequency: 78.5%
References:0
References:0
Frequency: 79.1%
References:1
References:1
(hide)
Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
Frequency: 81.2%
References:0
References:0
Frequency: 82.3%
References:0
References:0
Frequency: 85.8%
References:0
References:0
Frequency: 88.5%
References:0
References:0
Magnitude: 0
Frequency: 75.9%
Repute:Good
References:0
Frequency: 75.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:1
Frequency: 77.9%
Repute:Good
References:1
Magnitude: 0
Frequency: 78.8%
Repute:Good
References:0
Frequency: 78.8%
Repute:Good
References:0
Magnitude: 0
Frequency: 80.5%
Repute:Good
References:0
Frequency: 80.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:0
Frequency: 88.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:0
Frequency: 90.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 97.3%
Repute:Good
References:0
Frequency: 97.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:0
Frequency: 98.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
40 snps
(hide) Pain
Magnitude: 1.7
suggests you may be able to tolerate more pain than most people. However phased data may be necessary to increase certainty. See also gs232 gs233 gs234 gs235
Magnitude: 1.7
suggests you may be able to tolerate less pain than most people. However phased data may be necessary to increase certainty. See also gs232 gs233 gs234 gs235
reported to influence perception of pain
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rs6746030 is a SNP in the sodium channel Nav1.7 SCN9A gene. In five cohorts tested, totaling 1,277 individuals, the rarer rs6746030(A) allele was associated with increased pain (p=0.0001).
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 1p21.3; Reported Gene(s): NR; Risk Allele: rs6693882-?); (p-value= 0.000002).This variant is associated with Pain.] [GWAS:Pain]
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Genome-wide association study identifies a potent locus associated with human opioid sensitivity rs2952768(C) was associated with more analgesic requirements ... exhibited less vulnerability to severe methamphetamine or alcohol dependence, fewer eating disorders, and a lower ‘Reward Dependence’ score on a personality questionnaire. The (C;C) genotype was significantly associated with the elevated expression of a neighboring gene, CREB. SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. Our findings provide valuable information for the personalized treatment of pain and drug dependence. [GWAS:Opioid sensitivity]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 19p12; Reported Gene(s): LOC400680, ZNF429; Risk Allele: rs2562456-?); (p-value= 0.0000000002).This variant is associated with Pain.] [GWAS:Pain]
Frequency: 45.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 11q23.3; Reported Gene(s): NR; Risk Allele: rs17122021-?); (p-value= 0.0000007).This variant is associated with Pain.] [GWAS:Pain]
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
Magnitude: 0.1
You probably experience typical sensitivity to pain according to See also gs232, gs234, and gs235
3 genosets 8 snps
(hide) Personality
lack of empathy? You have a SNP in the oxytocin receptor which may make you less empathetic than most people. When under stress you may have more difficulty recognizing the emotional state of others which impacts loneliness, parenting, and socializing skills.
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rs53576 is a silent G to A change in the oxytocin receptor (OXTR) gene. The blog Not Exactly Rocket Science discusses that Americans with (G;G) tend to be more sensitive parents, more empathetic and less lonely than those with an ‘A’. In a Korean population people with (G;G) were less likely to seek support from their peers. Culture, distress, and oxytocin receptor polymorphism (OXTR) interact to influence emotional support seeking. Oxytocin receptor genetic variation relates to empathy and stress reactivity in humans. With a blog summary, shows that people with the (G;G) genotype were better able to discern the emotional state of others than those who carried the A-allele. Associations between the oxytocin receptor gene (OXTR) and affect, loneliness and intelligence in normal subjects. Ox...
somewhat more associated with impulsiveness and adult ADHD
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rs1611115 (C-1021T) is a SNP near the dopamine beta-hydroxylase (DBH) gene. per OMIM, the T allele is associated with lower DBH expression in plasma (16 of TT genotype had DBH activity of 4.1, 46 of CT genotype had DBH activity of 25.2, and 112 of CC genotype had DBH activity of 48.1 nmol/min/ml) Association tests related to affective disorders such as ADHD were performed using four independent samples, healthy volunteers (N = 387), patients with affective disorders (N = 182), adult attention deficit hyperactivity disorder (ADHD) patients (N = 407), and patients with personality disorders (N = 637). Personality disorder patients carrying the DBH TT genotype exhibited higher neuroticism and novelty seeking scores as compared to individuals with the (C;C) or (C;T) genotype. Analyses on the l...
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 2p22.1; Reported Gene(s): THUMPD2; Risk Allele: rs2540226-T); (p-value= 0.000003).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
higher risk for RA
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rs6313, also known as T102C, is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108 and gs226 Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. [PharmGKB:Curated Risk or phenotype-associated allele (s): T/T. Phenotype: Patients, with a diagnosis of probable Alzheimer's disease, carryi...
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Our findings suggest an influence of the gene in the neural substrate mediating sensorimotor gating and working memory, especially when combined with high anxiety. Genetic associations with schizophrenia: meta-analyses of 12 candidate genes. The neurobiology of D-amino acid oxidase and its involvement in schizophrenia. Persistence criteria for susceptibility genes for schizophrenia: a discussion from an evolutionary viewpoint.
normal
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rs1800759 is a SNP in the promoter (regulatory region) of the alcohol dehydrogenase 4 (ADH4) gene. In a study of 500+ patients with either alcohol dependence or drug dependence, rs1800759 was the most significant ADH4 SNP to be associated (in a recessive manner) with increased risk for either condition, at least in Caucasians. In another study, a five-factor model of personality in 243 subjects with substance dependence (175 European Americans [EAs] and 68 African Americans [AAs]), along with 296 healthy control subjects (256 EAs and 40 AAs), was conducted in association with an ADH4 SNP survey. rs1800759(A) alleles and (A;A) genotypes A/A were significantly associated with agreeableness scores.
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[GWAS:Personality]
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The G allele of SNAP25 gene SNP rs362584 was associated with increased neurotic traits (combined p value = 0.0000522) in a group of 3972 Sardinians, and two smaller replicative samples from the USA and Netherlands (the replicative samples were not significant by themselves, with the Netherlands sample showing considerably less of a trend).full paper in pdf
multiple associations, see details
(hide)
rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
(hide)
The A allele of the CLOCK gene SNP rs6832769 was associated with lessened agreeableness (p = 0.00000871) in a group of 3972 Sardinians. The effect remained significant in the replicative American sample, but failed to achieve significance in the Norwegian sample and third sample (though the combined p value remained significant at 0.000865). full paper in pdf [PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 4q12; Reported Gene(s): CLOCK; Risk Allele: rs6832769-A); (p-value= 0.000002).This variant is associated with Personality dimensions.]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: Xp11.3; Reported Gene(s): FUNDC1; Risk Allele: rs6610953-G); (p-value= 0.000006).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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[GWAS:Personality]
complex; possible association with anxiety related behaviours
(hide)
In mice, the genetic locus best correlated to anxiety-related behaviour contains the 'regulator of G protein signaling 2' gene . In humans, SNPs in the equivalent RGS2 gene have now been studied to see if they are correlated to anxiety related disorders. In the first part of one study, 119 families including children underwent standard lab-based behavioural assessments of behavioural inhibition, defined as a heritable temperamental profile characterized by a tendency to be shy, avoident, and behaviourally restrained in situations that are novel or unfamiliar. Along with some other RGS2 SNPs, carriers of a rs4606(G) allele were 3 fold more likely to exhibit behavioural inhibition (CI: 1.31-6.84, p = 0.0026). In the second part of this study, 744 college undergraduates (228 men, 516 women) w...
Magnitude: 0
References:10
References:10
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Rs35753505 (SNP8NRG221533) is located within the 5'-flanking region of the NRG1 (Neuregulin 1) gene. g2b2mh blog rs35753505(C;C) correlates with frontal brain having to working harder during a working memory task. personality traits - C allele carriers associated with higher (NEO-FFI) scores of neuroticism and lower scores of conscientiousness in a sample of 523 healthy individuals The results suggest that subjects with risk alleles show hyperactivations in areas associated with elaborate episodic memory encoding and retrieval strategies.
16 snps
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poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
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Also known as Ile462Val A4889G CYP1A1*2C Genome amplification of single sperm using multiple displacement amplification. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. Multilocus analysis of SNP and metabolic data within a given pathway. CYP1A1 and CYP1B1 polymorphisms and their association with estradiol and estrogen metabolites in women who are premenopausal and perimenopausal. Dietary phytoestrogen intake is associated with reduced colorectal cancer risk. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Cytochrome P450 1A1 (CYP1A1) polymorphisms and breast cancer risk in Korean women. Cor...
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[PharmGKB:Curated In an 80-patient study, this variant was not associated with plasma concentrations of montelukast or with response to treatment with montelukast.]
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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Association of the multidrug-resistance-associated protein gene (ABCC2) variants with intrahepatic cholestasis of pregnancy. Polymorphisms of MRP2 (ABCC2) are associated with susceptibility to nonalcoholic fatty liver disease. MRP2 and GSTP1 polymorphisms and chemotherapy response in advanced non-small cell lung cancer. Genetic polymorphisms influence mycophenolate mofetil-related adverse events in pediatric heart transplant patients. ADME pharmacogenetics: investigation of the pharmacokinetics of the antiretroviral agent lopinavir coformulated with ritonavir. Interindividual variability in hepatic expression of the multidrug resistance-associated protein 2 (MRP2/ABCC2): quantification by liquid chromatography/tandem mass spectrometry. A comprehensive study of polymorphisms in ABCB1, ABCC2...
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
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rs1801280 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801280(C). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
?
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common form...
may require more methadone during heroin withdrawal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
References:5
carrier of one CYP2D6*41 allele
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*3, defined as the common loss of function variant rs1057910(C) (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/. Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of nonsteroidal anti-inflammatory drugs (NSAIDs) that are CYP2C8 or CYP2C9 substrates, such as aceclofena...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
normal
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
normal/common
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rs2273697, also known as c1249G>A or p.V471I, is a nonsynonymous polymorphism in the ABCC2 gene. From an initial case-control study of 146 patients with epilepsy, followed by replication (p=0.001) in another 279 patients, the rs2273697(A) allele was associated with neurological adverse drug reactions from taking carbamazepine. Functional studies showed that this SNP selectively reduced carbamazepine transport across the cell membrane. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP showed a strong association with the neurological adverse drug reaction caused (ADR) by carbamazepine (P=0.005). The study results indicate that the c.1249A variant is an independent risk factor of carbamazepine CNS ADR. Study size: 146 patients with epilepsy who had been prescr...
normal
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rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well by the variant OATP1B1 protein encoded by the rs4149056(C) allele include: *Several cholesterol lowering statins, generally leading to reduced inh...
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
Magnitude: 0
Frequency: 75.2%
Repute:Good
References:14
Frequency: 75.2%
Repute:Good
References:14
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs11572080). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: In woman, the risk of acute myocardial infarction (AMI) tended to be higher for subjects carrying the CYP2C8*3*3 genotype versus *1*1 (OR = 1.9). The CYP2C8*3 variants are 416G>A (rs10509681) and 1196A>G (rs11572080). Tested in all subjects, the risk of AMI was also higher in individuals carrying the CYP2C8*3 allele (*3*3; *1*3 versus*1*1) [1.2 (1.0-1.5...
Magnitude: 0
Frequency: 77.1%
Repute:Good
References:15
Frequency: 77.1%
Repute:Good
References:15
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs10509681). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with increased risk for neurotoxicity with paclitaxel treatment. Study size: 132. Study population/ethnicity: Patients with Neoplasms receiving paclitaxel; Spain. Significance metric(s): HR = 1.54 (0.96-2.47); p = 0.072. Type of association: PK; TOX.]
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
common in complete genomics
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[PharmGKB:In-Depth A study of 124 White patients, which received a high-dose regimen consisting of cyclophosphamide, thiotepa and carboplatin as intravenous infusions, concludes patients homozygous for the GSTP1 C341T allele may have enhanced exposure to thiotepa and tepa.]
normal
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The rs3758581(A) SNP defines a CYP2C19 allele known as V331I. Analysis of 50 SNPs in CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOF mass spectrometry in Chinese Han population.
common in complete genomics
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rs776746, also known as 6986G>A, is a SNP encoding the (nonfunctional) CYP3A5*3 allele of the CYP3A5 gene. CYP3A5*3 has been studied especially in connection with the metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. The optimal therapeutic dose is in a relatively narrow window, so blood concentration monitoring is recommended. CYP3A5*3 carriers tend to build up higher levels of tacrolimus than CYP3A5*1 carriers, unless their tacrolimus intake is reduced. Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Prevalence of common dis...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: CYP2B6*2 genotype in the transplant recipient was associated with hemorrhagic cystitis. Study size:107 . Study population/ethnicity: Donors and patients with leukemia after HLA-identical hematopoietic stem cell transplantation, France. Significance metric(s): p = 0.03. Type of association: TOX]
common in complete genomics
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[PharmGKB:Curated Increased risk for smokers to develop gastric cancer, no association for breast cancer.]
common in complete genomics
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[PharmGKB:Curated This variant is in exon 1b of ABCB1 and may be associated with tacrolimus pharmacokinetics in renal transplant recipients. It was also associated with lower ABCB1 mRNA expression and possibly being an useful invasive marker predicting poorly-differentiated colorectal adenocarcinomas and thereby the poor prognosis of the Japanese patients in the study.]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: results from the Spanish Bladder Cancer Study and meta-analyses. Genetic variation in N-acetyltransferase 1 (NAT1) and 2 (NAT2) and risk of non-Hodgkin lymphoma.
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
normal
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rs9332130, also known as 815A>G, 10598A>G or E272G, is a SNP in the CYP2C9 gene. The rs9332130(G) allele defines the CYP2C9*10 variant.
normal
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rs2256871, also known as 752A>G, 10535A>G or H251R, is a SNP in the CYP2C9 gene. The rs2256871(C) allele defines the CYP2C9*9 variant.
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
common in complete genomics
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CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. [PharmGKB:In-Depth This variant decreases enzyme activity and affects metabolism of coumarin and nicotine; part of the CYP2A6*17 haplotype.]
common in complete genomics
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23andMe reports that the T allele of rs3918290 is associated with the rare recessive disorder dihydropyrimidine dehydrogenase deficiency (DPD), also known as hereditary thymine-uraciluria or familial pyrimidinemia. pharmgkb - defines *2A allele, which has a significantly higher chance of 5-fluorouracil toxicity Fluorouracil Toxicity [PharmGKB:In-Depth Heterozygosity for the A allele of this SNP is associated with mucositis and leukopenia drug toxicity in cancer patients treated with fluorouracil. Heterozygous males were more likely than heterozygous females to develop severe toxicity. In this study, no A/A homozygotes were observed.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:7
Frequency: 100.0%
Repute:Good
References:7
normal
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rs10264272, also known as 14690G>A, is a SNP in the CYP3A5 gene. indicates that this corresponds with CYP3A5*6, however, this seems doubtful. CYP3A5 allele nomenclature found at http://www.cypalleles.ki.se/cyp3a5.htm indicates that CYP3A5*6 (also known as 14690G>A) is a splicing defect resulting in essentially no activity in the gene. This does not correspond with dbSNP, which indicates that is a nucleotide substition (624G-A) which only results in a 'silent' substitution of AAG (Lysine) to AAA (Lysine). [PharmGKB:In-Depth Nonfunctional allele present predominantly in the African American population.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
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rs12720461 is a SNP in the CYP1A2 gene. The rs12720461(T) allele defines the CYP1A2*1K_-729C>T variant. [PharmGKB:Curated Likely disrupts transcription factor binding, leading to reduced function.]
normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
common in complete genomics
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[PharmGKB:Non-Curated Increased sensitivity to inhibition by TBA in oocytes]
normal
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rs9332239, also known as 1465C>T, 50338C>T or P489S, is a SNP in the CYP2C9 gene. The rs9332239(T) allele defines the CYP2C9*12 variant. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504.
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Reduced metformin and MPP+ uptake in transfected cells]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs28371706, also known as 1023C>T or T107I, is a SNP in the CYP2D6 gene. The rs28371706(T) allele is found in several CYP2D6 variants: * CYP2D6*17 decreased activity variant * CYP2D6*40 non-functioning variant * CYP2D6*58 variant * CYP2D6*64 variant [PharmGKB:In-Depth Variant was identified as being part of the reduced function haplotype CYP2D6*17.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the *10 haplotype and affects nicotine metabolism.]
Magnitude: 0
Repute:Good
References:10
Repute:Good
References:10
common in complete genomics
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[PharmGKB:In-Depth Risk or phenotype-associated allele: TC. Phenotype: This variant is statistically correlated with the mean of maximum transaminase values (ALT) in patients from Mozambique, with ALT mean value of 91.68 U/l for TT, and 221.45 U/l for TC genotypes (p < 0.001). Study size: 156. Study population/ethnicity: HIV infected patients from Mozambique. Significance metric(s): p< 0.001. Type of association: GN; CO]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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Suspect: Variation suspected to be false positive due to artifacts of the presence of a paralogous sequence in the genome (Musumeci et al. 2010) (Sudmant et al. 2010) or evidence suggested sequencing error or computation artifacts. [PharmGKB:Curated The CYP2B6:1132C>T variant results in a truncated protein and high plasma levels of efavirenz in patients.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279854, also known as 29748T>C or F446S, is a SNP in the CYP3A5 gene. The rs41279854(G) allele defines the CYP3A5*10 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
normal
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rs5030867, also known as 2935A>C or H324P, is a SNP in the CYP2D6 gene. The rs5030867(C) allele defines the CYP2D6*7 variant, which is inactive.
common in complete genomics
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[PharmGKB:In-Depth This variant affects heat stability and affects nicotine metabolism; part of the CYP2A6*7 and CYP2A6*10 haplotypes.]
normal
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rs7900194, also known as 449G>A, 3627G>A or R150H, is a SNP in the CYP2C9 gene. The rs7900194(A) allele defines the CYP2C9*8 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a mod...
common in complete genomics
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common in complete genomics
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[PharmGKB:Curated The variant is part of the CYP2C8*2 allele. In an in vitro study, the CYP2C8*2 allele exhibited a two-fold lower clearance for paclitaxel than the wildtype.]
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
common in complete genomics
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[PharmGKB:Non-Curated Reduced metformin and MPP+ uptake in transfected cells]
75 snps
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poorer metabolizer of several popular medicines; patients prescribed Plavix get less benefit, and have higher risk for adverse cardiovascular events
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
warfarin sensitivity (~2.5 mg/day)
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rs8050894, is located on chromosome 16 in the gene VKORC1. VKORC1 is the primary target of the drug warfarin (Coumadin), a commonly used oral anticoagulant. rs8050894 is one of several polymorphisms found in VKORC1 that is associated with specific warfarin doses (). Other polymorphisms in VKORC1 (rs7196161, rs9923231, rs9934438, rs2359612) are equally predictive of warfarin dose requirement in both European and Asian-descent individuals. Other polymorphisms found in the gene cytochrome P450 2C9 (CYP2C9) influence the metabolism of warfarin and have a smaller effect on warfarin dose. These polymorphisms are rs1799853 (CYP2C9*2) and rs1057910 (CYP2C9*3). In several hundred Europeans, no association was found between rs8050894 and risk for ischemic stroke. Genetic-based dosing in orthopedic p...
Magnitude: 2
Frequency: 43.1%
References:10
Frequency: 43.1%
References:10
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
Homozygous for CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
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Also known as Ile462Val A4889G CYP1A1*2C Genome amplification of single sperm using multiple displacement amplification. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. Multilocus analysis of SNP and metabolic data within a given pathway. CYP1A1 and CYP1B1 polymorphisms and their association with estradiol and estrogen metabolites in women who are premenopausal and perimenopausal. Dietary phytoestrogen intake is associated with reduced colorectal cancer risk. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Cytochrome P450 1A1 (CYP1A1) polymorphisms and breast cancer risk in Korean women. Cor...
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association of the rs7483 SNP with late-onset Alzheimer's disease
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[PharmGKB:Non-Curated altered kinetics of gemcitabine in transfected cells]
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rs1051740, also known as Tyr113His, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. severe hypersensitivity syndrome, triggered by carbamazepine in the presence of a concomitant active human herpes virus (HHV) 6 and 7 infection with the allele HLA-A*3101 and rs1051740(C;C) [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a logistic regression model adjusted for history of phenytoin use during the first trimester and maternal epilepsy, the maternal EPHX1 113 H (rs1051740 T/C) allele was associated with craniofacial abnormalities in the child. Study size: 157 pregnancies. Study population/ethnicity: phenytoin use during the first trimester and maternal epilepsy. metric(s): per rare allele OR: 2.43, 95% confidence interval (CI): 1.16-5.10, P=0.02. Type of asso...
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[PharmGKB:In-Depth May be associated with a higher warfarin dose phenotype]
CYP1A2_1545T>C homozygote
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rs2470890 is a SNP in the CYP1A2 gene. The rs2470890(C) allele defines the CYP1A2_1545T>C variant. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [PharmGKB:Curated Weakly associated with tardive dyskinesia and schizophrenia.]
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Role of the PXR gene locus in inflammatory bowel diseases. Polymorphisms in NF-kappaB, PXR, LXR, PPARgamma and risk of inflammatory bowel disease. Pregnane X receptor (PXR/NR1I2) gene haplotypes modulate susceptibility to inflammatory bowel disease. Variants of the human NR1I2 (PXR) locus in chronic periodontitis.
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells]
Frequency: 17.9%
References:3
References:3
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rs700518 is a SNP potentially linked in a gender-specific manner to hypertension [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A1:1576T>C (N521D) SNP, the C (521Asp) allele was at frequency was 0.47 and 0.00 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 94) and African (n = 91) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SLC10A2:rs2301159 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.01 Type of association: CO; TOX]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ABCC6 rs2238472 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX] [OMIM:PSEUDOXANTHOMA ELASTICUM]
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rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele. influences the risk of breast cancer according to the 23andMe blog 23andMe blog rs1800566 increases susceptibility to Lung cancer 0.48 times for heterozygotes (CT) [PharmGKB:Curated Risk or phenotype-associated allele: C/T. Phenotype: There was no association between the NQO1*2 polymorphism and the risk of anthracycline-related CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 1.04; p = 0.97. Type of association: CO; TOX; ADR.] [OMIM:NAD(...
None
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
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Association of the multidrug-resistance-associated protein gene (ABCC2) variants with intrahepatic cholestasis of pregnancy. Polymorphisms of MRP2 (ABCC2) are associated with susceptibility to nonalcoholic fatty liver disease. MRP2 and GSTP1 polymorphisms and chemotherapy response in advanced non-small cell lung cancer. Genetic polymorphisms influence mycophenolate mofetil-related adverse events in pediatric heart transplant patients. ADME pharmacogenetics: investigation of the pharmacokinetics of the antiretroviral agent lopinavir coformulated with ritonavir. Interindividual variability in hepatic expression of the multidrug resistance-associated protein 2 (MRP2/ABCC2): quantification by liquid chromatography/tandem mass spectrometry. A comprehensive study of polymorphisms in ABCB1, ABCC2...
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[PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: There was a trend toward an association between the CBR3 V244M polymorphism and the risk of CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 8.16, p = 0.056 (G/G vs A/A); OR = 5.44, p = 0.092 (G/A vs A/A). Type of association: CO; TOX; ADR.]
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rs1041983 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1041983(T). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
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rs4646(A) allele carriers with breast cancer being treated with letrozole are reported to do worse than rs4646(C;C) patients, based on a study of (only) 95 women. [PharmGKB:Curated A study in 67 patients with hormone receptor-positive metastatic breast cancer treated with letrozole, the presence of this SNP in the 3' untranslated region of the CYP19A1 gene is associated with improved treatment efficacy.]
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[OMIM:?]
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*2.]
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CYP17 genotype is associated with short menstrual cycles, early oral contraceptive use and BRCA mutation status in young healthy women. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. The rs743572 common variant in the promoter of CYP17A1 is not associated with prostate cancer risk or circulating hormonal levels. CYP17 genetic variation and risk of breast and prostate cancer from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3). Genetic polymorphisms in CYP17, CYP3A4, CYP19A1, SRD5A2, IGF-1, and IGFBP-3 and prostate cancer risk in African-American men: the Flint Men's Health Study. Genetic variation in CYP17 and endometrial cancer risk. Variants in hormone biosynthesis genes an...
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Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene. Cholesterol 7alpha-hydrolase (CYP7A1) c.-278A>C promoter polymorphism in gallstone disease patients. CYP7A1 (-204 A>C; rs3808607 and -469 T>C; rs3824260) promoter polymorphisms and risk of gallbladder cancer in North Indian population. Promoter variant -204A > C of the cholesterol 7alpha-hydroxylase gene: association with response to plant sterols in humans and increased transcriptional activity in transfected HepG2 cells.
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous CDA:79A>C (K27Q) SNP, the C allele (27Gln) was at frequency 0.36 and 0.04 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001) Study size: 180. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 85) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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[OMIM:?]
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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[PharmGKB:Curated This variant is in the promoter region of UGT1A1 and associated with serum bilirubin levels and hyperbilirubinemia in a genome wide association scan from 4300 Sardinian individuals.] [GWAS:Bilirubin levels]
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
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rs1799929 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799929(T). When this SNP is indicative of carrying a NAT2*5A allele, the following may be relevant: A study (based on only 42 patients) found that women with the NAT2*5A slow genotype (which presumably means rs1799929(T;T)) had a significantly higher risk of cervical cancer compared with individuals with the NAT2*5A fast genotype (i.e. carriers of only one rs1799929(T) allele), with a reported odds ratio of 7.469 (CI: 1.6-33.3, p=0.008). [PharmGKB:Curated in vitro study; PK: 20-fold reduction...
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rs10046 is a SNP potentially linked in a gender-specific manner to hypertension rs10046(C;C) associated with miscarriages (P = 0.017) Polymorphisms associated with circulating sex hormone levels in postmenopausal women. Multilocus analysis of SNP and metabolic data within a given pathway. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Sex and body mass index specific regulation of blood pressure by CYP19A1 gene variants. Genome-wide association with bone mass and geometry in the Framingham Heart Study. Single nucleotide polymorphisms of the aromatase gene (CYP19A1), HER2/neu status, and prognosis in breast cancer patients. Association between single-nucleotide polymorphisms in hormone metabolism and DNA repai...
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
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Parkinson's disease The risk alleles for each SNP identified from conditional logistic regression, rs1721100 C, rs1721082 T and rs1799836 A, are consistent with previous reports. Significant interaction between this MAOB SNP and a FGF20 SNP, rs1721100 was also noticed.
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs4148950 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.024 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.
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rs1801280 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801280(C). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148943 C variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0001 Type of association: PD; CO]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs1871450 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.048 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. Univariate/multivariate genome-wide association scans using data from families and unrelated samples. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Tests of association for quantitative traits in nuclear families using principal components to correct for population stratification. Family-based bivariate association tests for quantitative traits. A comparative study of three methods for detecting association of quantitative traits in samples of related subjects. Family-based genome-wide association study for simulated data of Framingham Heart Study. The Genetic Analysis Workshop 16 Problem 3: simulat...
Frequency: 52.3%
References:6
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: CBR3 11G>A variant was associated with lower doxorubicinol AUC, lower CBR3 expression in breast tumor tissue, greater tumor reduction, and greater percentage reduction of leukocyte and platelet counts at nadir. Study size: 101 Study population/ethnicity: Asian; patients with Breast Neoplasms; Chinese; Malay; Indian Significance metric(s): p = 0.009 (AUC); p = 0.001 (expression); p = 0.015 (tumor reduction); p = 0.03 (leukocyte and platelet counts). Type of association: PK; TOX]
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[PharmGKB:Curated UGT1A7:-57T>G increases risk of anemia in irinotecan-treated patients.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs1883322 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0061 Type of association: PD; CO]
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common trait being optimism [GWAS:Common traits (Other)]
?
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common form...
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rs1051266 (Arg27Cys, 80G>A) is a snp within SLC19A1 (Solute carrier family 19 (folate transporter), member 1). Cys (A) allele associated with reduced plasma folate women with GA and AA genotypes had higher red blood cell folate concentrations, not significantly associated with serum folate or homocysteine levels methotrexate (antifolate drug) uptake lowest in individuals with GG genotype than those with GA or AA genotypes [PharmGKB:Curated Risk or phenotype-associated allele: SLC19A1 80GG (27Arg/Arg) and GA (27His/Arg)>AA (27His/His) genotypes. Phenotype: A composite pharmacogenetic index (additive from zero to five) was calculated using the following values: ATIC 347CC or TSER*3/*3 or SLC19A1 80GG or SLC19A1 80GA genotypes were valued as 0, ATIC 347CG or TSER*2/*3 or SLC19A1 80AA g...
Frequency: 56.6%
References:3
References:3
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[PharmGKB:Non-Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
may require more methadone during heroin withdrawal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
Frequency: 57.5%
References:7
References:7
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*4.]
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non sig. gwas, hit (p = 3 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SPG7:rs12960 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.004 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the SLC28A1:1383C>T SNP, the T allele was at frequency was 0.08 and 0.05 in Europeans and Africans, respectively. There was no significant difference between ethnic groups in genotype frequency distribution (p > 0.05). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 91) and African (n = 94) descent. Significance metric(s): Not significant, p > 0.05. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs6922548 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0011 Type of association: PD; CO]
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[GWAS:Cataracts in type 2 diabetes]
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The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Influence and interaction of genetic polymorphisms in catecholamine neurotransmitter systems and early life stress on antidepressant drug response.
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
References:1
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[PharmGKB:Curated In a study of ovarian cancer patients (n=104) receiving a cisplatin-cyclophosphamide regimen, the AGG/AGG genotype (insertion) of GSTM3 intron 6 insertion/deletion was associated with decreased incidence of thrombocytopenia, anemia and neuropathy.]
References:1
effects of higher bilirubin; irinotecan toxicity; tranilast toxicity http://web.me.com/russbaltman/Site/PharmGKBlog/Entries/2010/10/24_Updated_Irinotecan_Label.html
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Although the insertion is supposed to be the minor allele, the majority of FTDNA v2 and 23andMe v2 results show II as the result, so use caution when interpreting this result. rs34815109 is one of four SNPs all describing an insertion/deletion polymorphism in the promoter region of the UGT1A1 gene. This gene encodes a protein that modifies hepatic bilirubin in order to allow it to be excreted. SNPs that reduce the activity of the UGT1A1 gene therefore tend to increase serum bilirubin levels. The rs34815109(TA) allele represents the insertion variant, which actually adds a seventh (TA) pair to what is already a string of six (TA) pairs; this reduces the activity to 30% of normal, and is thus the risk allele. The risk allele is commonly referred to as the UGT1A1*28 allele, and it is homozygo...
References:1
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[PharmGKB:Curated Associated with significantly lower AUC ratio of SN38G/SN38, high incidence of severe diarrhea, but not tumor response.]
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Cytochrome P450 2C8 pharmacogenetics: a review of clinical studies. [PharmGKB:Curated The allelic variant is designated as CYP2C8*12 allele.]
References:1
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rs41303343, also known as 27131_27132insT, is a SNP in the CYP3A5 gene. The rs41303343(T) allele defines the CYP3A5*7 variant, which is nonfunctional.
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Important Variant Information for CYP2J2. involved in metabolism of some drugs. rs890293, also known as -50C>T, is a SNP in the CYP2J2 gene. A study of 5,740 participants of the cardiovascular cohort of the 'Malmö Diet and Cancer' study was monitored for cardiovascular events over 10 years, with the conclusion being there was no significant association between this SNP and either hypertension or ischemic events. [PharmGKB:In-Depth Although this promoter SNP is the most-studied CYP2J2 variant, its in vivo effects remain unclear due to conflicting experimental findings.]
References:5
carrier of one CYP2D6*41 allele
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
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rs212090(A;T) (T;T) increased cancer susceptibility (OR, 1.37; 95% CI, 1.03-1.83)
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rs1062033 increases susceptibility to Osteoporosis, postmenopausal for carriers of the G allele Common variations in estrogen-related genes are associated with severe large-joint osteoarthritis: a multicenter genetic and functional study. [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SULT1C2: rs1402467 G variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0083 Type of association: PD; CO]
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X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ATP7A:rs2227291 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX]
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[PharmGKB:Curated A study in 1,090 Caucasian prostate cancer cases found significant associations involved CYP3A43 P340A genotypes and history of benign prostatic hyperplasia (BPH). These results of the study suggest that androgen metabolism may act in concert with inflammatory phenotypes such as BPH in determining prostate cancer severity.]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*3, defined as the common loss of function variant rs1057910(C) (NM_000771:c.430C>T, NP_000762:p.144R>C) [http://www.pharmgkb.org/search/annotatedGene/cyp2c9/. Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of nonsteroidal anti-inflammatory drugs (NSAIDs) that are CYP2C8 or CYP2C9 substrates, such as aceclofena...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-1 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[PharmGKB:In-Depth This variant results in a truncated protein and no enzyme activity; part of the CYP2A6*20 haplotype.]
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
normal
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The rs5787121(-) (i.e. deletion) SNP defines the CYP2C19 allele known as G439- or 90052delG.
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
normal
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
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risk of aortic calcification was calculated, adjusted for potential confounders. The T allele frequency of the VKORC1 1173C>T polymorphism was 38.8%. 1185 (37.2%) persons were homozygous CC, 1529 (48,0%) were heterozygous CT and 473 (14.8%) were homozygous TT. Persons with at least one T-allele had a statistically significant 19% (95% CI 2 to 40%) risk increase of calcification of the aortic far wall compared to CC homozygous persons [PharmGKB:Curated Double homozygous VKORC1 1173T/T, CYP4F2 433Val/Val (n = 5) showed the highest INR (3.1; 2.0-4.7) and required the lowest acenocoumarol dose (11 ± 3 mg/week) The addition of the V433M genotype to the VKORC1 genotype raised the R2 from 8% to 14% for INR, and from 12% to 19% for acenocoumarol dose requirements.] [OMIM:VITAMIN K EPOXIDE...
normal
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rs1056836, also known as 4326C/G, Val432Leu or L432V, is a SNP in the cytochrome P450 1B1 (CYP1B1) gene. This gene is a member of the CYP1 gene family and one of the major enzymes involved in the hydroxylation of estrogens, a reaction likely to be relevant in hormonal carcinogenesis. [In dbSNP orientation, the (C) allele encodes the Leu; the (G) the Val.] In a study of 153 Hispanic Caucasians with prostate cancer the rs1056836(G;G) genotype showed decreased risk compared to the more common (C;C) genotype (odds ratio = 0.31, p = 0.04, CI: 0.10-0.96). This report cites another study as indicating that rs1056836(C;C) high-risk stage III and IV breast cancer patients receiving dose-intense paclitaxel in combination with doxorubicin and cyclophosphamide experience a longer progression-free surv...
common in complete genomics
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Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria.
common in complete genomics
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rs272893 and rs273900 are associated with Crohn's disease (OR 2.16; 95% CI 1.21-3.59 and OR 2.40; 95% CI 1.43-4.05)
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
normal
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
7x more likely to respond to certain antidepressants
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rs2235015 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is near 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. rs2235015 has an r<sup>2</sup> value of >0.5 with this group. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported ...
normal/common
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rs2273697, also known as c1249G>A or p.V471I, is a nonsynonymous polymorphism in the ABCC2 gene. From an initial case-control study of 146 patients with epilepsy, followed by replication (p=0.001) in another 279 patients, the rs2273697(A) allele was associated with neurological adverse drug reactions from taking carbamazepine. Functional studies showed that this SNP selectively reduced carbamazepine transport across the cell membrane. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP showed a strong association with the neurological adverse drug reaction caused (ADR) by carbamazepine (P=0.005). The study results indicate that the c.1249A variant is an independent risk factor of carbamazepine CNS ADR. Study size: 146 patients with epilepsy who had been prescr...
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs32440(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, the results we...
Magnitude: 0
Frequency: 65.5%
Repute:Good
References:4
Frequency: 65.5%
Repute:Good
References:4
common on affy axiom data
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[PharmGKB:Curated Subjects homozygous for this genotype showed decreased response to fluvastatin]
common on affy axiom data
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[OMIM:CYTOCHROME P450, SUBFAMILY I, POLYPEPTIDE 1; CYP1B1]
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rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes. [OMIM:PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-GAMMA, COACTIVATOR 1, ALPHA;]
normal
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rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well by the variant OATP1B1 protein encoded by the rs4149056(C) allele include: *Several cholesterol lowering statins, generally leading to reduced inh...
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
7x less likely to respond to certain antidepressants
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rs2235040 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2235040 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The CYP4B1:rs4646487 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.008 Type of association: CO; TOX]
normal
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rs2515641 is a SNP in the CYP2E1 gene. The rs2515641(T) allele defines the CYP2E1_10463T>C(F421F) variant.
Magnitude: 0
Frequency: 75.2%
Repute:Good
References:14
Frequency: 75.2%
Repute:Good
References:14
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs11572080). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: In woman, the risk of acute myocardial infarction (AMI) tended to be higher for subjects carrying the CYP2C8*3*3 genotype versus *1*1 (OR = 1.9). The CYP2C8*3 variants are 416G>A (rs10509681) and 1196A>G (rs11572080). Tested in all subjects, the risk of AMI was also higher in individuals carrying the CYP2C8*3 allele (*3*3; *1*3 versus*1*1) [1.2 (1.0-1.5...
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SPG7:rs2292954 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0004 Type of association: CO; TOX]
common in complete genomics
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Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. Glucocorticoid receptor gene variant in the 3' untranslated region is associated with multiple measures of blood pressure. Cohort profile: risk patterns and processes for psychopathology emerging during adolescence: the ROOTS project. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients. Association of FKBP5 gene haplotypes with completed suicide in the Japanese population. Glucocorticoid receptor polymorphism is associated with lithium response in bipolar patients.
Magnitude: 0
Frequency: 77.1%
Repute:Good
References:15
Frequency: 77.1%
Repute:Good
References:15
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs10509681). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with increased risk for neurotoxicity with paclitaxel treatment. Study size: 132. Study population/ethnicity: Patients with Neoplasms receiving paclitaxel; Spain. Significance metric(s): HR = 1.54 (0.96-2.47); p = 0.072. Type of association: PK; TOX.]
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:1
Frequency: 77.9%
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated The CYP3A43*1B allele is characterized by the silent 1150C>T substitution exon 11.]
common on affy axiom data
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[PharmGKB:Curated Drug efflux and cell surface expression (by MRK-16 and C219 probes) of P-gp was not different between wild-type and variant forms (single mutants: N21D, F103L, S400N, A893S, A998T, and double mutants: 21D-S400N, N21D-A893S, and S400N-A893S) in an in vitro vaccinia virus-based transient expression system. Fluroescent substrates included calcein AM, bodipy-FL-forskolin, bodipy-FL-verapamil, bodipy-FL-vinblastine, bodipy-FL-prazosin, bisantrene, and bodipy-FL-paclitaxel. There was a slight increase in wild-type P-gp efflux of bodipy-FL-paclitaxel over mutants.]
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: Carriers of either one or two alleles of the A allele required 19% lower warfarin maintenance dose (2.6 ± 1.3 mg) compared to GG homozygotes (3.2 ± 1.6 mg) (p < 0.0001). The combined effect of variants in four genes, as well as age, explained 26.6% of the overall interindividual warfarin dose variability, with VKORC1 (rs9923231 A allele) accounting for 19.1%, CYP2C9 (rs1799853 T allele, or rs1057910 C allele) for 3.2%, EPHX1 (rs2292566 A allele) for 1.7%, CYP4F2 (rs2108622 C allele) gentoypes for 1.1%, and age for 1.5%. Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French ce...
common in clinvar
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Variations in the peroxisome proliferator-activated receptor-gamma gene and melanoma risk. PPAR-gamma gene polymorphisms and psoriatic arthritis. The Genetics of PPARG and the Skeleton. The association of Pro12Ala polymorphism of peroxisome proliferator-activated receptor-gamma gene with serum osteoprotegerin levels in healthy Korean women. Association of stearoyl-CoA desaturase 1 activity with familial combined hyperlipidemia. Polymorphism of genes related to insulin sensitivity and the risk of biliary tract cancer and biliary stone: a population-based case-control study in Shanghai, China. PPAR Genomics and Pharmacogenomics: Implications for Cardiovascular Disease. Association of FTO with obesity-related traits in the Cebu Longitudinal Health and Nutrition Survey (CLHNS) Cohort. Differen...
common in complete genomics
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[PharmGKB:In-Depth A study of 124 White patients, which received a high-dose regimen consisting of cyclophosphamide, thiotepa and carboplatin as intravenous infusions, concludes patients homozygous for the GSTP1 C341T allele may have enhanced exposure to thiotepa and tepa.]
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rs2066853 has been associated with increased risk for colorectal polyps depending on the amount of meat eaten or overall exposure to heterocyclic amines. lung cancer in a Chinese population heterozygous rs2158041 OR=1.53 for GA vs compared with the (G;G) and rs7811989 OR=1.48 for (G;A) compared with the GG genotype) *rs2066853 (p.Arg554Lys) and cumulative cigarette smoking and the Lys/Lys genotype conferred an increased risk of lung cancer in the heavy smokers OR=3.36 [PharmGKB:In-Depth Very common variant with controversial associations.]
common on affy axiom data
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[PharmGKB:Curated The DPYD:496A>G variant was associated with toxicity of fluoropyrimidine-based chemotherapy in patients with gastroesophageal and breast cancer, but did not reach significance in patients with colorectal malignancies.]
normal
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rs6413420 is a SNP in the CYP2E1 gene. The rs6413420(T) allele defines the CYP2E1*7_-71G>T variant.
normal
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rs2031920 is a SNP in the CYP2E1 gene. The rs2031920(T) allele defines the CYP2E1_-1055C>T variant. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
common in complete genomics
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The association reported in was not replicated in . Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients. Molecular mechanism of glucocorticoid resistance in inflammatory bowel disease. Genetic polymorphisms of the glucocorticoid receptor may affect the phenotype of women with anovulatory polycystic ovary syndrome.
normal
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The rs3758581(A) SNP defines a CYP2C19 allele known as V331I. Analysis of 50 SNPs in CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOF mass spectrometry in Chinese Han population.
common in complete genomics
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[PharmGKB:Curated The g.22,060G variant segregates with g.23,238C>T (with one exception). The allele containing both of these polymorphisms has been designated FMO2*2C.]
common in complete genomics
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rs776746, also known as 6986G>A, is a SNP encoding the (nonfunctional) CYP3A5*3 allele of the CYP3A5 gene. CYP3A5*3 has been studied especially in connection with the metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. The optimal therapeutic dose is in a relatively narrow window, so blood concentration monitoring is recommended. CYP3A5*3 carriers tend to build up higher levels of tacrolimus than CYP3A5*1 carriers, unless their tacrolimus intake is reduced. Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Prevalence of common dis...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: CYP2B6*2 genotype in the transplant recipient was associated with hemorrhagic cystitis. Study size:107 . Study population/ethnicity: Donors and patients with leukemia after HLA-identical hematopoietic stem cell transplantation, France. Significance metric(s): p = 0.03. Type of association: TOX]
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:3
Frequency: 92.9%
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: UGT1A8*3 (defining allele: 830A, 277Tyr). Phenotype: In vitro catalytic activity and protein expression. Genetic analysis of UGT1A8 (exclusively expressed in extrahepatic tissue) in 69 individuals identified four alleles, of which UGT1A8*3 was defined as having tyrosine at amino acid 277. In vitro studies in HEK293 cells show UGT1A8*3 (830A, 277Y) has a dramatic reduction in catalytic activity compared to wildtype, but no loss in protein expression. Study size: 69. Study population/ethnicity: Lung cancer patients and family members and other volunteers who served as controls. Type of association: GN; FA]
normal
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rs2070672 is a SNP in the CYP2E1 gene. The rs2070672(G) allele defines the CYP2E1*7_-352A>G variant.
common in complete genomics
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[PharmGKB:Curated Increased risk for smokers to develop gastric cancer, no association for breast cancer.]
common in complete genomics
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[PharmGKB:Curated This variant is in exon 1b of ABCB1 and may be associated with tacrolimus pharmacokinetics in renal transplant recipients. It was also associated with lower ABCB1 mRNA expression and possibly being an useful invasive marker predicting poorly-differentiated colorectal adenocarcinomas and thereby the poor prognosis of the Japanese patients in the study.]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP19A1*4. It is associated with significant decreases in levels of activity compared with the wild-type (WT) enzyme after transient expression in COS-1 cells.]
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[PharmGKB:Curated Drug efflux and cell surface expression (by MRK-16 and C219 probes) of P-gp was not different between wild-type and variant forms (single mutants: N21D, F103L, S400N, A893S, A998T, and double mutants: 21D-S400N, N21D-A893S, and S400N-A893S) in an in vitro vaccinia virus-based transient expression system. Fluroescent substrates included calcein AM, bodipy-FL-forskolin, bodipy-FL-verapamil, bodipy-FL-vinblastine, bodipy-FL-prazosin, bisantrene, and bodipy-FL-paclitaxel. There was a slight increase in wild-type P-gp efflux of bodipy-FL-paclitaxel over mutants.]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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[PharmGKB:Curated system: membrane vessicles from HEK cells transfected with WT or variant; FA: variant had approx 50% decrease in transport of tritium labelled 17[beta]-estradiol-17[beta]-D-glucuronide and tritium labelled methotrexate]
Magnitude: 0
Frequency: 95.6%
Repute:Good
References:2
Frequency: 95.6%
Repute:Good
References:2
normal
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rs6413419, also known as 4768G>A or V179I, is a SNP in the CYP2E1 gene. The rs6413419(A) allele defines the CYP2E1*4 variant.
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a study of bacterial expressed and purified human CBR3 proteins, the 93Ile variant had significantly reduced maximal reaction velocity (V(max)) for both anthracyclines compared with the wild-type enzyme. Type of association: FA.]
common in complete genomics common for Caucasians on the 23andme platform
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rs1801279 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801279(A). [PharmGKB:Curated Homozygous A allele is slow acetylator phenotype (altered rates of metabolism of arylamines). May be associated with higher risk for bladder cancer and lower risk for colorectal cancer.]
common in complete genomics
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[PharmGKB:Curated Human lymphocyte cell lines homozygous for the A allele of this variant, common in Japanese populations, exhibit reduced surface membrane levels of ABCC4 protein and increased sensitivity to 6-mercaptopurine toxicity relative to cell lines homozygous for the G allele. The A-allele and G-allele cell lines have similar overall protein expression levels.]
common in complete genomics
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NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: results from the Spanish Bladder Cancer Study and meta-analyses. Genetic variation in N-acetyltransferase 1 (NAT1) and 2 (NAT2) and risk of non-Hodgkin lymphoma.
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:1
Frequency: 98.2%
Repute:Good
References:1
normal
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rs28365083, also known as 27289C>A, is a SNP in the CYP3A5 gene. The rs28365083(A) allele defines the CYP3A5*2 variant, which is nonfunctional. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Genotyping panel for assessing response to cancer chemotherapy. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism.
common in complete genomics
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[PharmGKB:Curated The variant is located in the promoter region of the GSTP1 gene and was significantly associated with the level of GSTP1 mRNA in Mexican Americans. The G(-18)A variant is tightly linked with the well studied Ile 105 Val polymorphism, which is associated with various clinical phenotypes.]
normal
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rs9332130, also known as 815A>G, 10598A>G or E272G, is a SNP in the CYP2C9 gene. The rs9332130(G) allele defines the CYP2C9*10 variant.
normal
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rs2256871, also known as 752A>G, 10535A>G or H251R, is a SNP in the CYP2C9 gene. The rs2256871(C) allele defines the CYP2C9*9 variant.
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: Kinetic studies using purified, histidine-tagged, recombinant enzymes demonstrated that the V88I mutation leads to a significantly reduced maximal rate of activity for doxorubicin and daunorubicin compared to wild type protein. Type of association: FA]
normal
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rs2069526 is a SNP in the CYP1A2 gene. The rs2069526(T) allele defines the CYP1A2*1K_-739T>G variant. [PharmGKB:Curated Present in reduced function haplotype, unlikely to be causative.]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
common in complete genomics
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CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. [PharmGKB:In-Depth This variant decreases enzyme activity and affects metabolism of coumarin and nicotine; part of the CYP2A6*17 haplotype.]
common in complete genomics
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23andMe reports that the T allele of rs3918290 is associated with the rare recessive disorder dihydropyrimidine dehydrogenase deficiency (DPD), also known as hereditary thymine-uraciluria or familial pyrimidinemia. pharmgkb - defines *2A allele, which has a significantly higher chance of 5-fluorouracil toxicity Fluorouracil Toxicity [PharmGKB:In-Depth Heterozygosity for the A allele of this SNP is associated with mucositis and leukopenia drug toxicity in cancer patients treated with fluorouracil. Heterozygous males were more likely than heterozygous females to develop severe toxicity. In this study, no A/A homozygotes were observed.]
normal
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rs4986909, also known as 1247C>T, 22026C>T or P416L, is a SNP in the CYP3A4 gene. The rs4986909(T) allele defines the CYP3A4*13 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*13; in vitro, this allele did not result in detectable P450 holoprotein.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:7
Frequency: 100.0%
Repute:Good
References:7
normal
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rs10264272, also known as 14690G>A, is a SNP in the CYP3A5 gene. indicates that this corresponds with CYP3A5*6, however, this seems doubtful. CYP3A5 allele nomenclature found at http://www.cypalleles.ki.se/cyp3a5.htm indicates that CYP3A5*6 (also known as 14690G>A) is a splicing defect resulting in essentially no activity in the gene. This does not correspond with dbSNP, which indicates that is a nucleotide substition (624G-A) which only results in a 'silent' substitution of AAG (Lysine) to AAA (Lysine). [PharmGKB:In-Depth Nonfunctional allele present predominantly in the African American population.]
normal
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rs1041988 is a SNP in the CYP3A4 gene. The rs1041988(C) allele defines the CYP3A4*_23139T>C(I431T) variant.
normal
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rs1057909 is a SNP in the CYP2C9 gene. The rs1057909(G) allele defines the CYP2C9_42612A>G variant, about which little is known.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Greatly reduced the efficiency of metabolism of carvedilol.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
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rs12720461 is a SNP in the CYP1A2 gene. The rs12720461(T) allele defines the CYP1A2*1K_-729C>T variant. [PharmGKB:Curated Likely disrupts transcription factor binding, leading to reduced function.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated study of 54 livers; variant not associated with altered midazolam clearance]
normal
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rs3091339 is a SNP in the CYP3A4 gene. The rs3091339(G) allele defines the CYP3A4*_11460A>G(K96E) variant.
normal
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rs3208363 is a SNP in the CYP3A4 gene. The rs3208363(G) allele defines the CYP3A4*_16907T>G(S252A) variant.
normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
normal
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rs4986907, also known as 485G>A, 14269G>A or R162Q, is a SNP in the CYP3A4 gene. The rs4986907(A) allele defines the CYP3A4*15A variant. [PharmGKB:In-Depth Defining variant for CYP3A4*15A.]
normal
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rs4986913, also known as 1399C>T, 23237C>T or P467S, is a SNP in the CYP3A4 gene. The rs4986913(T) allele defines the CYP3A4*19 variant. [PharmGKB:In-Depth Part of CYP3A4*19.]
common in complete genomics
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[PharmGKB:Curated Homozygous A allele is slow acetylator phenotype.]
normal
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rs4987161, also known as 566T>C, 15615T>C or F189S, is a SNP in the CYP3A4 gene. The rs4987161(C) allele defines the CYP3A4*17 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*17, defective in metabolizing the hypertensive drug nifedipine in vitro; exhibited lower turnover numbers than wild-type for testosterone and chlorpyrifos in vitro.]
normal
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The rs6413438(T) allele defines the CYP2C19 allele known as CYP2C19*10. This allele may lead to reduced metabolism of S-mephenytoin at least in vitro. [PharmGKB:Curated This variant is the defining SNP for CYP2C19*10. This variant is associated with reduction in the metabolism of S-mephenytoin in vitro.]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for the FMO2*1 and FMO2*2 alleles. The major allele, FMO2*2, is characterized by a T at genomic position 23,238 and encodes a truncated inactive protein. The minor allele, FMO2*1, has a C at this position and encodes a full-length active protein. Thus, this SNP could potentially be associated with differential drug response.]
normal
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Tests for th...
common in complete genomics
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[PharmGKB:Non-Curated Increased sensitivity to inhibition by TBA in oocytes]
common in complete genomics
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[PharmGKB:Non-Curated Increased sensitivity to inhibition by TBA in oocytes]
normal
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rs915909 is a SNP in the CYP2E1 gene. The rs915909(T) allele defines the CYP2E1_6498C>T(I321I) variant.
normal
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rs9332239, also known as 1465C>T, 50338C>T or P489S, is a SNP in the CYP2C9 gene. The rs9332239(T) allele defines the CYP2C9*12 variant. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504.
G6PD Type B
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23andMe blog G6PD Deficiency [PharmGKB:Curated Causes a slight decrease in G6PD activity.] [OMIM:G6PD A+]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated Reduced uptake of estrone sulfate and methotrexate in oocytes] [GWAS:None]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Reduced metformin and MPP+ uptake in transfected cells]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs12721634, also known as 44 T>C or L15P, is a SNP in the CYP3A4 gene. The rs12721634(C) allele defines the CYP3A4*14 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*14.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated altered substrate specificity with respect to inosine and uridine]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17882687(C) SNP defines the CYP2C19 allele known as CYP2C19*15, and also known as CYP2C19_55A>C or I19L.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17884712(A) allele defines the CYP2C19 variant known as CYP2C19*9, which is associated with a slight decrease in the metabolism of S-mephenytoin (at least in vitro). [PharmGKB:Curated This variant is the defining SNP for CYP2C19*9 and associated with a modest decrease in the V(max) for 4'-hydroxylation of S-mephenytoin in vitro.]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
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rs2279343, also known as Lys262Arg, is a SNP within the CYP2B6 gene. variants including the Arg allele include CYP2B6*4, CYP2B6*6, and CYP2B6*7 Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Cyclophosphamide-metabolizing enzyme polymorphisms and survival outcomes after adjuvant chemotherapy for node-positive breast cancer: a retrospective cohort s...
normal
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The rs2740574(G) allele encodes a variant form of CYP3A4 known as CYP3A4*1B. rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM A pooled study (1,400+ samples) along with a replication study conducted by members of the Ovarian Cancer Association Consortium found a 2.5-2.8x increased risk for ovarian cancer] for rs2740574(G;G) individuals (CI: 1.2-6.5, p=0.017). The authors note that CYP3A4 encodes a key enzyme in estrogen metabolism and which may be linked to ovarian carcinogenesis. [PharmGKB:Curated Risk or phenotype-associated allele: CYP3A4*1B, rs2740574 G allele. Phenotype: CYP3A4*1B (rs2740574 G) allele carriers show a significantly increased risk for SCLC (OR = 2.25, p = 0.02), which showed a...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated (i) Decreased intracellular calcein levels (increased function), (ii) increased intracellular BODIPy-FL- paclitaxel levels (decreased function), in transfected cells]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs28371706, also known as 1023C>T or T107I, is a SNP in the CYP2D6 gene. The rs28371706(T) allele is found in several CYP2D6 variants: * CYP2D6*17 decreased activity variant * CYP2D6*40 non-functioning variant * CYP2D6*58 variant * CYP2D6*64 variant [PharmGKB:In-Depth Variant was identified as being part of the reduced function haplotype CYP2D6*17.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28371759, also known as 878T>C, 20070T>C or L293P, is a SNP in the CYP3A4 gene. The rs28371759(C) allele defines the CYP3A4*18 variant. [PharmGKB:Curated In a study of 2,178 women of ages 40-79 years, this variant in the CYP3A4 gene was significantly associated with low bone mass. In vitro functional analyses indicate that CYP3A4*18 is a gain-of-function mutation in sex steroid metabolism, resulting in rapid oxidation of estrogens and testosterone.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs28383468, also known as 3705C>T or H30Y, is a SNP in the CYP3A5 gene. The rs28383468(T) allele defines the CYP3A5*H30Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28383479, also known as 19386G>A, is a SNP in the CYP3A5 gene. The rs28383479(A) allele defines the CYP3A5*9 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28399424, also known as 5090C>T or R431W, is a SNP in the CYP1A2 gene. The rs28399424(T) allele defines the CYP1A2*6 decreased activity variant. [PharmGKB:Curated Reduced expression.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the *10 haplotype and affects nicotine metabolism.]
Magnitude: 0
Repute:Good
References:10
Repute:Good
References:10
common in complete genomics
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[PharmGKB:In-Depth Risk or phenotype-associated allele: TC. Phenotype: This variant is statistically correlated with the mean of maximum transaminase values (ALT) in patients from Mozambique, with ALT mean value of 91.68 U/l for TT, and 221.45 U/l for TC genotypes (p < 0.001). Study size: 156. Study population/ethnicity: HIV infected patients from Mozambique. Significance metric(s): p< 0.001. Type of association: GN; CO]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs3208361 is a SNP in the CYP3A4 gene. The rs3208361(G) allele defines the CYP3A4*_15635A>G(I193V) variant.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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Suspect: Variation suspected to be false positive due to artifacts of the presence of a paralogous sequence in the genome (Musumeci et al. 2010) (Sudmant et al. 2010) or evidence suggested sequencing error or computation artifacts. [PharmGKB:Curated The CYP2B6:1132C>T variant results in a truncated protein and high plasma levels of efavirenz in patients.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: CYP2B6 mRNA expression and bupropion hydroxylase activity were approximately 2-fold higher in livers genotyped -82TC as in those genotyped -82TT. Study size: 85 (expression); 77 (activity). Study population/ethnicity: Non-tumorous liver samples from White individuals, Germany. Significance metric(s): p = 0.007 (expression); p = 0.042 (activity). Type of association: FA; PD]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated cell based studies; enhanced basal activity on cyp3a4 transcription wrt WT]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated The CYP2B6*27 allele shows an 85% decrease in enzyme activity leading to high plasma levels of efavirenz in patients.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279854, also known as 29748T>C or F446S, is a SNP in the CYP3A5 gene. The rs41279854(G) allele defines the CYP3A5*10 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279857, also known as 7298C>A or S100Y, is a SNP in the CYP3A5 gene. The rs41279857(T) allele defines the CYP3A5*S100Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
common in complete genomics
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[PharmGKB:In-Depth Subjects with the G variant showed higher plasma pravastatin AUC and Cmax relative to A variant]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: Kinetic studies using purified, histidine-tagged, recombinant enzymes demonstrated that the P131S mutation leads to decreased catalytic efficiency (Kcat/Km) for doxorubicin and daunorubicin compared to wild type protein. Type of association: FA]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated Reduced thymidine uptake in oocytes]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
normal
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rs4986908 is a SNP in the CYP3A4 gene. The rs4986908(A) allele defines the CYP3A4*_14313G>A(E174H) variant. [PharmGKB:In-Depth Defining variant for CYP3A4*10.]
normal
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rs4986910, also known as 1334T>C, 23171T>C or M445T, is a SNP in the CYP3A4 gene. The rs4986910(C) allele defines the CYP3A4*3 variant. [PharmGKB:In-Depth Risk or phenotype-associated allele: CYP3A4*3 (rs4986910) 445Thr, 1334 C allele Phenotype: Two patients taking tacrolimus carried the CYP3A4*3 (445Thr) allele. The tacrolimus dose-adjusted C(0) in these 2 patients was higher than that in patients with the wild-type (455 Met/Met) genotype (n = 62), as follows: 134.9 (106.6-163.2) versus 83.83 (33.83-397.8) ng/mL per mg/kg, respectively. This difference was also observed at 12 months after transplantation, as follows: 147.3 (117.0-177.5) versus 88.79 (26.0-432.0) ng/mL per mg/kg. Study size: 64. Study population/ethnicity: Renal transplant recipients from the outpatient clinic of th...
normal
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rs5030867, also known as 2935A>C or H324P, is a SNP in the CYP2D6 gene. The rs5030867(C) allele defines the CYP2D6*7 variant, which is inactive.
common in clinvar
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rs5030868 is SNP located on the X-Chromosome associated with moderate to severe Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency. Often referred to as the “Mediterranean variant”, the 563C->T mutation encodes a non-synonymous Serine to Phenylalanine substitution at Amino Acid position 188 (S188F) resulting in reduced catalytic efficiency and stability G6PD . In red blood cells, G6PD acts as the primary electron source for reactions that neutralize reactive oxygen species; thus the red blood cells of G6PD deficient individuals are especially susceptible to damage from oxidative stress . The Mediterranean variant of G6PD has been associated with acute hemolytic anemia induced by the ingestion of fava beans, glibenclamide, primaquine, dapsone, and Aspirin among others. <br><br&...
common in complete genomics
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[PharmGKB:In-Depth This variant affects heat stability and affects nicotine metabolism; part of the CYP2A6*7 and CYP2A6*10 haplotypes.]
common in complete genomics
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Direct molecular haplotyping of multiple polymorphisms within exon 4 of the human catechol-O-methyltransferase gene by liquid chromatography-electrospray ionization time-of-flight mass spectrometry.
normal
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rs2070673 is a SNP in the CYP2E1 gene. The rs2070673(A) allele defines the CYP2E1*7_-333T>A variant.
normal
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rs1573496 is a SNP in the ADH7 alcohol dehydrogenase 7 gene. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1573496(G) allele has a protective effect. Carriers of this allele had a 0.68x (decreased; p=10<sup>-9</sup>) risk of having one of these cancer types. A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium. The data in this paper, makes it seem that (G;G) was much more common. This is inconsistent with the HapMap frequencies, suggesting the sequence may have been flipped. Diplotype trend regression analysis of the ADH gene cluster and the ALDH2 gene: multiple significant associations with alcohol dependence. Multiple ADH genes modulat...
common in complete genomics
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
normal
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Also known as CYP2E1_-1295G>C, this SNP is reported to mark the c2 allele of CYP2E1. The rs3813867(C) allele defines the CYP2E1_-1295G>C variant allele. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
normal
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rs1057911 is a SNP in the CYP2C9 gene. The rs1057911(T) allele defines the CYP2C9_50298A>T variant, about which little is known. Warfarin
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common in complete genomics
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[PharmGKB:Curated The variant is part of the CYP2C8*2 allele. In an in vitro study, the CYP2C8*2 allele exhibited a two-fold lower clearance for paclitaxel than the wildtype.]
common in complete genomics
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[PharmGKB:Non-Curated Increased resistance to daunorubicin, doxorubicin, valinomycin, or actinomycin D in transformed yeast]
normal
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rs12721627, also known as 554C>G, 15603C>G or T185S, is a SNP in the CYP3A4 gene. The rs12721627(G) allele defines the CYP3A4*16 variant. [PharmGKB:Curated in vitro study; PK: variant shows substrate altered kinetics compared to wild type]
normal
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
common in clinvar
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[OMIM:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, MONTREAL TYPE]
common in clinvar
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[OMIM:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, GARY TYPE]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP8A1*1C haplotype.]
common in complete genomics
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rs6413413, also known as Thr60Ser, is a SNP in the alcohol dehydrogenase 1B ADH1B gene. The rs6413413(A) allele is the more common, encoding the amino acid threonine (Thr); the quite rare rs6413413(T) allele encodes the variant serine (Ser). On it's own, this SNP is said to explain 2.5% of the variability in the rate at which alcohol is metabolized, based on a study of 250 Spaniards. More significantly (in a statistical sense), this study concluded that combinations of this SNP and others were shown to affect alcohol metabolism; most of these combinations are represented by the gs211 genoset. Note that the effects of alcohol are higher in individuals who break down (basically, detoxify) ethanol more slowly.
278 snps
(hide) Placebo
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
1 snp
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Frequency: 0.0%
References:1
References:1
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[GWAS:QT interval]
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[GWAS:QT interval]
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QT interval rs3807375 rs2880058 [GWAS:QT interval]
Frequency: 10.6%
References:28
References:28
Long QT interval
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rs10494366, a SNP in the NOS1AP gene encoding the nitric oxide synthase I adaptor protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10494366(G) allele was associated with a 3.8-ms (CI: 3.0 - 4.6ms, p=7.8x10(-20)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 mi...
Frequency: 14.2%
References:1
References:1
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rs10494366, rs4657139 and rs16847548 were significantly associated with adjusted QT interval in whites. relative hazard of SCD associated with each C allele at rs16847548 was 1.31. rs12567209 was also independently associated with SCD in whites (relative hazard 0.57, 95% confidence interval 0.39 to 0.83, P=0.003). No significant associations observed in blacks. Multiple independent genetic factors at NOS1AP modulate the QT interval in a multi-ethnic population. Genetic variation in NOS1AP is associated with sudden cardiac death: evidence from the Rotterdam Study.
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[GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 26.6%
References:3
References:3
1.3x increased risk for sudden cardiac death in Caucasians
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rs16847548 and rs16856785 strongly associated with QT interval Based on a large study of 19,000+ adults, SNPs rs10494366, rs4657139 and rs16847548 were significantly associated with adjusted QT interval in whites but not in African-Americans. The relative hazard of sudden cardiac death (SCD) associated with each rs16847548(C) allele was 1.31 (CI: 1.10 - 1.56, p=0.002). rs12567209 was also independently associated with SCD in whites (relative hazard 0.57, CI: 0.39 - 0.83, p=0.003).
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[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs7142881-A). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
Frequency: 33.9%
References:1
References:1
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 16q21; Reported Gene(s): CNOT1,GINS3, NDRG4, SLC38A7, GOT2; Risk Allele: rs37062-G); (p-value= 3E-25).This variant is associated with QT interval.] [GWAS:QT interval]
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QT interval rs3807375 rs2880058 [PharmGKB:Curated QT prolongation] [GWAS:Electrocardiographic traits]
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 7q36.1; Reported Gene(s): KCNH2; Risk Allele: rs2968863-T); (p-value= 0.000000000000002).This variant is associated with QT interval.] [GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 16q21; Reported Gene(s): NDRG4; Risk Allele: rs7188697-A); (p-value= 7E-25).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4799915-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
Frequency: 46.9%
References:2
References:2
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 6q22.31; Reported Gene(s): c6orf204,SLC35F1, PLN, ASF1A; Risk Allele: rs11756438-A); (p-value= 5E-22).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 47.8%
References:3
References:3
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Common variants at ten loci influence QT interval duration in the QTGEN Study. [PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 17q24.3; Reported Gene(s): KCNJ2; Risk Allele: rs17779747-T); (p-value= 0.000000000006).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 49.6%
References:4
References:4
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 3p22.2; Reported Gene(s): SCN5A; Risk Allele: rs12053903-C); (p-value= 0.00000000000001).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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New atypical antipsychotics for schizophrenia: iloperidone. [PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs993648-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 1q23.3; Reported Gene(s): NOS1AP; Risk Allele: rs4657178-T); (p-value= 7E-33).This variant is associated with QT interval.] [GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 16p13.13; Reported Gene(s): LITAF,CLEC16A, SNN, ZC3H7A, TNFRSF17; Risk Allele: rs8049607-T); (p-value= 0.000000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 59.3%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 3p22.2; Reported Gene(s): SCN5A; Risk Allele: rs11129795-A); (p-value= 0.00000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Curated Associated with altered myocardial repolarization.] [GWAS:Electrocardiographic traits]
Frequency: 63.7%
References:3
References:3
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 11p15.5; Reported Gene(s): KCNQ1; Risk Allele: rs12296050-T); (p-value= 0.00000000000000003).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 63.7%
References:1
References:1
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 7q36.1; Reported Gene(s): KCNH2; Risk Allele: rs4725982-T); (p-value= 0.0000000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 71.7%
References:3
References:3
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 1q23.3; Reported Gene(s): NOS1AP; Risk Allele: rs12029454-A); (p-value= 3E-45).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 72.6%
References:2
References:2
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 11p15.5; Reported Gene(s): KCNQ1; Risk Allele: rs12576239-T); (p-value= 0.000000000000001).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 81.4%
References:1
References:1
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 99.1%
References:1
References:1
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[GWAS:QT interval]
Longer QT interval
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rs10918594, a SNP near the NOS1AP gene encoding the nitric oxide synthase I protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10918594(G) allele was associated with a 3.6-ms (CI: 2.7 - 4.4ms, p=6.9x10(-17)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 minor ho...
Magnitude: 0
Frequency: 75.8%
Repute:Good
References:3
Frequency: 75.8%
Repute:Good
References:3
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 1q24.2; Reported Gene(s): ATP1B1; Risk Allele: rs10919071-A); (p-value= 0.000000000000001).This variant is associated with QT interval.] [GWAS:QT interval]
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:1
Frequency: 86.7%
Repute:Good
References:1
Magnitude: 0
Frequency: 88.3%
Repute:Good
References:1
Frequency: 88.3%
Repute:Good
References:1
common on affy axiom data
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 11p15.5; Reported Gene(s): KCNQ1; Risk Allele: rs2074238-T); (p-value= 0.00000000000000003).This variant is associated with QT interval.] [GWAS:QT interval]
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4933824-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
common in complete genomics
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23andMe blog Influences QT interval [PharmGKB:Curated Associated with noise-induced hearing loss.] [OMIM:POTASSIUM CHANNEL, VOLTAGE-GATED, ISK-RELATED SUBFAMILY, MEMBER 1;]
common in clinvar
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[PharmGKB:In-Depth Has been studied in association with long QT.] [OMIM:LONG QT SYNDROME 3, ACQUIRED, SUSCEPTIBILITY TO]
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs3924426-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 6q22.31; Reported Gene(s): PLN; Risk Allele: rs12210810-C); (p-value= 0.00000000000000002).This variant is associated with QT interval.] [GWAS:QT interval]
common in complete genomics
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rs16847548 and rs16856785 strongly associated with QT interval
63 snps
(hide) Redheads
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
Magnitude: 0
References:0
References:0
normal
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This missense mutation influences red hair color and has been observed in the Spanish maternal ancestry of User:Corpas son.
common in complete genomics
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rs1805006, known as Asp84Glu or D84E, is one of several SNPs in the MC1R gene associated with higher risk of melanoma. The risk allele is rs1805006(A), compared with the wild-type rs1805006(C) allele. Allelic odds ratio for pale skin(P-value)=5.19(<1.0e-5)MC1R*D84E rs1805006 http://genepi.qimr.edu.au/contents/p/staff/Duffyetal_JID_520-528Jan10.pdf See also OMIM 155555.0003 [OMIM:?]
4 snps
(hide) Revised NEO Personality Inventory
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 2p22.1; Reported Gene(s): THUMPD2; Risk Allele: rs2540226-T); (p-value= 0.000003).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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The G allele of SNAP25 gene SNP rs362584 was associated with increased neurotic traits (combined p value = 0.0000522) in a group of 3972 Sardinians, and two smaller replicative samples from the USA and Netherlands (the replicative samples were not significant by themselves, with the Netherlands sample showing considerably less of a trend).full paper in pdf
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The A allele of the CLOCK gene SNP rs6832769 was associated with lessened agreeableness (p = 0.00000871) in a group of 3972 Sardinians. The effect remained significant in the replicative American sample, but failed to achieve significance in the Norwegian sample and third sample (though the combined p value remained significant at 0.000865). full paper in pdf [PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 4q12; Reported Gene(s): CLOCK; Risk Allele: rs6832769-A); (p-value= 0.000002).This variant is associated with Personality dimensions.]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: Xp11.3; Reported Gene(s): FUNDC1; Risk Allele: rs6610953-G); (p-value= 0.000006).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
4 snps
(hide) SERPINA1
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finds no association between rs709932 and pulmonary emphysema [OMIM:PI M4]
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finds no association between rs1303 and pulmonary emphysema [OMIM:PI M3] [GWAS:Metabolite levels]
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finds no association between rs8004738 and pulmonary emphysema
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finds no association between rs11832 and pulmonary emphysema
Frequency: 52.7%
References:2
References:2
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finds no association between rs17751769 and pulmonary emphysema
common in complete genomics
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Alpha 1-antitrypsin deficiency, emphysema, and liver disease. Genetic basis and strategies for therapy. Molecular analysis of the heterogeneity among the P-family of alpha-1-antitrypsin alleles. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in complete genomics
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rs28929474, also known as Glu342Lys as well as E366K, is a SNP in the serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 gene. This SNP is the one most frequently leading, when homozygous, to the complications of alpha-1 antitrypsin deficiency and the associated high risk of emphysema and liver disease. Between 1 - 2% of US Caucasians are thought to be (heterozygous) carriers for this SNP, leading some associations, like the Alpha-1 Foundation, to call for mass carrier screening. * 23andMe blog rs28929474(T) increases odds of liver disease in cystic fibrosis patients by 4.17 times. (T;T) at both copies of this SNP causes alpha-1 antitrypsin deficiency; note use of opposite strand nomenclature by this company. finds no association between rs28929474...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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rs28931568 is a SNP representing an amino acid change in the SERPINA1 gene, which encodes alpha-1-antitrypsin (AAT). Carriers of two rs28931568(A) alleles, i.e. homozygotes, are at high risk for emphysema based on the finding of this variant in an affected African-American family. [OMIM:PI M(MINERAL SPRINGS)]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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rs28931569 is a SNP representing an amino acid change in the SERPINA1 gene, which encodes alpha-1-antitrypsin (AAT). Carriers of two rs28931569(C) alleles, i.e. homozygotes, are at high risk for emphysema . [OMIM:PI M(PROCIDA)]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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rs17580, also known as the S allele, is a SNP in the SERPINA1 gene. Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. See rs28929474 for the most common pathologic SNP in the SERPINA1 gene. finds no association between rs17580 and pulmonary emphysema a relatively small study of 182 patients found no association between rs17580 and risk for cholangiocarcinoma Alpha-1 Antitrypsin Deficiency [OMIM:PI S]
18 snps
(hide) Skin color
probably light-skinned, European ancestry This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.
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This SNP influences skin pigmentation. The allele p.A111T, rs1426654(A), indicates light-skinned european ancestry. It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned. This SNP is one of three from the SLC24A5 gene that can be analyzed to categorize the ancestry of a person as either European, African, or Asian, based on a 2009 study. The 3 SNPs are: * rs1426654 * rs2555364 * rs16960620 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER]
normal
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Although the rs26722(T) alllele is relatively rare, at least statistically it seems to be associated with darker eye, hair, and skin color, all other things being equal. A genomewide association study of skin pigmentation in a South Asian population. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Association of the SLC45A2 gene with physiological human hair colour variation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Genetic determinants of hair and eye colours in the Scottish and Danish populations. [OMIM:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
generally non-European, but if European, 7x more likely to have black hair
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pi...
3 snps
(hide) SLC6A2
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T allele associated with better response to treatment of ADHD with atomoxetine.
may be associated with ADHD
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T allele may be associated with Attention deficit hyperactivity disorder.
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G allele associated with better response to treatment of ADHD with atomoxetine.
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A allele associated with better response to treatment of ADHD with atomoxetine.
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Sexually dimorphic effects of four genes (COMT, SLC6A2, MAOA, SLC6A4) in genetic associations of ADHD: a preliminary study.
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Support for association between ADHD and two candidate genes: NET1 and DRD1.
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(Associated with ADHD.)
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Trajectories of change in depression severity during treatment with antidepressants. Pharmacogenomics of antidepressant drugs.
Frequency: 72.6%
References:3
References:3
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Norepinephrine transporter and catecholamine-O-methyltransferase gene variants and attention-deficit/hyperactivity disorder symptoms in adults. Further evidence of association between two NET single-nucleotide polymorphisms with ADHD. Lack of association between response of OROS-methylphenidate and norepinephrine transporter (SLC6A2) polymorphism in Korean ADHD. Genetic influences on attention deficit hyperactivity disorder symptoms from age 2 to 3: a quantitative and molecular genetic investigation. Support for association between ADHD and two candidate genes: NET1 and DRD1.
common in complete genomics
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G allele associated with better response to treatment of ADHD with atomoxetine.
Magnitude: 0
Frequency: 98.5%
Repute:Good
References:3
Frequency: 98.5%
Repute:Good
References:3
common in complete genomics
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The data were consistent for rs11568324, suggesting the existence of a rare allele conferring protection for ADHD
normal
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rs5558 (F528C) is a non-synonymous SNP in SLC6A2 (norepinephrine transporter), with a T encoding for Phenylalanine and C encoding the rare Cysteine variant. assoc. w/ major depression Cysteine variant exhibited increased norepinephrine transport, insensitivity to protein kinase C induced down-regulation, and a decrease in desipramine (tricyclic antidepressant) potency
20 snps
(hide) Squecco List
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[haplogroup:?]
Frequency: 100.0%
References:0
References:0
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[haplogroup:?]
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[haplogroup:?]
(hide)
this snp is on the 23andMe microarray but lacks a dbSNP identifier. It is on the Squecco List
References:0
(hide)
[haplogroup:?]
(hide)
[haplogroup:?]
(hide)
[haplogroup:?]
(hide)
[haplogroup:?]
References:0
References:0
(hide)
[haplogroup:?]
References:0
References:0
References:0
References:0
(hide)
[haplogroup:?]
(hide)
[haplogroup:?]
(hide)
[haplogroup:?]
(hide)
[haplogroup:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
(hide)
[haplogroup:?]
31 snps
(hide) Test Trails A
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
Frequency: 53.6%
References:2
References:2
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 5 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 4 x 10^-6) for Test Trails A performance [GWAS:Cognitive Performance]
Frequency: 79.6%
References:2
References:2
(hide)
non sig. gwas, hit (p = 3 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
Magnitude: 0
Frequency: 91.1%
Repute:Good
References:2
Frequency: 91.1%
Repute:Good
References:2
common in complete genomics
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non sig. gwas, hit (p = 7 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
6 snps
(hide) Tetrahydrobiopterin
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? T allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. C allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. C allele associated with higher tolerance to pain.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. T allele associated with higher tolerance to pain.
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Examination of tetrahydrobiopterin pathway genes in autism. Examination of association to autism of common genetic variation in genes related to dopamine.
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Do genetic predictors of pain sensitivity associate with persistent widespread pain? C allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. A allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. A allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? A allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
6 snps
(hide) Tooth Development
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Tooth Development [GWAS:None]
Frequency: 25.0%
References:0
References:0
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Rs17179670 is a SNP implicated in Tooth Development
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Tooth Development [GWAS:None]
3 snps
(hide) TPMT
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[PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.1013 (ANOVA); p = 0.0159 (QMIS); p = 0.0178 (KW) Type of association: PK.]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
5 snps
(hide) Variable number tandem repeat
common in complete genomics
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- rs2227902 and rs3796530 were found to be in 100% LD with a variable number tandem repeat (VNTR) length variant in the REST gene in a sample of 746 elderly Caucasians. Minor alleles (T and A, respectively) at both locations associated with the 4-length VNTR, while common alleles associated with the VNTR 5-length repeat. Carriers of the 4-length VNTR homozygous for the Val66 variant in the BDNF gene performed slightly, but significantly (p = 0.004), better than those without in the general cognitive tests performed in the study. Carriers of the 5-length VNTR and the 66Met BDNF variant had significantly lower g (p = 0.01), but the effect was not as great as the individual effect of the 66Met allele.
1 snp
(hide) Vitamin D
a statistically significantly increased risk for proximal colorectal cancer among those with at least one A allele (OR=1.42; 95% CI=1.03-1.97).
Frequency: 3.5%
References:6
References:6
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Genome-wide association with bone mass and geometry in the Framingham Heart Study. Vitamin D receptor gene polymorphisms and epithelial ovarian cancer risk. CDX2 VDR polymorphism and colorectal cancer. Vitamin D receptor gene haplotypes and susceptibility to HIV-1 infection in injection drug users. Vitamin D receptor gene polymorphisms and haplotypes and postmenopausal breast cancer risk. Association of vitamin D receptor gene variants, adiposity and colon cancer. Modification of the inverse association between dietary vitamin D intake and colorectal cancer risk by a FokI variant supports a chemoprotective action of Vitamin D intake mediated through VDR binding. Circulating 25-hydroxyvitamin D, VDR polymorphisms, and survival in advanced non-small-cell lung cancer. Colon tumor mutations an...
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rs3847987 in the vitamin D pathway was associated with the time to onset of COPD. The SNP is a cytosine-to-adenine switch, and men with two copies of the adenine variant were more likely to develop COPD. The hazard ratio was 1.60, with a 95% confidence interval from 1.26 to 2.05, which was significant at P=0.005. news
Frequency: 25.7%
References:2
References:2
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select biomarker trait being 25(OH) vitamin D plasma levels [GWAS:Select biomarker traits]
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[PharmGKB:In-Depth Associated with response to bronchodilators]
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A study of 414 (ex)-smokers older than 50 years concluded that vitamin D levels were reduced by 25% in rs7041](T;T) homozygotes (p<0.0001), and even after correction for age, gender and smoking history, they were also at increased risk for chronic obstructive pulmonary disease (COPD; odds ratio 2.11, CI: 1.20-3.71, p=0.009). They conclude that since vitamin D deficiency occurs frequently in COPD and correlates with its severity, vitamin D supplementation may be warranted in patients with severe COPD, and especially in those carrying rs7041(T) alleles. [OMIM:?]
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rs2107301 is a SNP in the vitamin D VDR receptor gene. rs2107301(T;T) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
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Variants in the vitamin D receptor gene and asthma. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the vitamin D receptor and their associations with risk of schizophrenia and selected anthropometric measures. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Vitamin D receptor gene (VDR) associations with cancer. Genome-wide association with bone mass and geometry in t...
Frequency: 38.1%
References:5
References:5
normal
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A very small study of 117 healthy European peri- and postmenarcheal girls (14.9 +/- 1.6 years) were followed for 4 years along with their calcium intake. Girls with rs4516035(C;T) and (C;C) genotypes had 13% lower spine mineral content if their milk intakes were below 260 mL/day, compared to either genotype-matched girls with higher milk intakes or to girls with the (T;T) genotype. If this is real, it suggests that rs4516035(C;T) and (C;C) female teens need more milk than rs4516035(T;T) girls to have optimal bone density. rs4516035 and the more aggressive tumour location in head-neck and trunk (OR=1.54, p=0.020)
Frequency: 42.7%
References:2
References:2
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rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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Levels of 25-hydroxyvitamin D in familial longevity: the Leiden Longevity Study. Concluded that familial longevity was associated with a lower vitamin D levels and a lower frequency of the allelic variation in the CYP2R1 gene. Genome-wide association study of circulating vitamin D levels. This SNP is part of CYP2R1, which encodes a key C-25 hydroxylase that converts vitamin D3 to an active vitamin D receptor ligand. This SNP, along with rs2282679, rs3829251, and rs6599638 accounted for 2.8% of the variance in circulating vitamin D levels. [GWAS:Vitamin D levels]
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Vaccine immunogenetics: bedside to bench to population. Personalized vaccines: the emerging field of vaccinomics. Toll-like receptor signaling pathway variants and prostate cancer mortality. Association of polymorphisms in TLR genes and in genes of the Toll-like receptor signaling pathway with cancer risk. [PharmGKB:Curated Heterozygots for this variant -926 bp in promoter region of the TLR3 gene were associated with low antibody and lymphoproliferative responses (p <or= 0.02) to measles vaccination.]
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[GWAS:Vitamin D levels]
Frequency: 82.3%
References:1
References:1
2.47x higher risk for prostate cancer
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rs2238135 is a SNP in the vitamin D VDR receptor gene. rs2238135(G;G) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
common in clinvar
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see rs2282679, a near-perfect proxy for rs4588 Gene-environment interaction effects on the development of immune responses in the 1st year of life. The genetics of chronic obstructive pulmonary disease. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. The Gc2 allele of the vitamin D binding protein is associated with a decreased postmenopausal breast cancer risk, independent of the vitamin D status. Genetic and environmental determinants of 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D levels in Hispanic and African Americans. Genetic polymorphisms of the vitamin D binding protein and plasma concentrations of 25-hydroxyvitamin D in premenopausal women. A meta-analysis of candidate gene polymorphisms and ischemic stroke in ...
normal
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rs2282679, located in the group-specific component (vitamin D binding protein) GC gene on chromosome 4p12, has been linked by several studies to vitamin D serum concentrations. In both studies, the allele associated with lower vitamin D, and thus the potential for vitamin D insufficiency, is rs2282679(C). Carriers of two such alleles have lower vitamin D than carriers of one allele, who in turn on average have lower vitamin D levels than rs2282679(A;A) individuals. A near-perfect proxy (i.e. substitute) for rs2282679 is reported to be rs4588. [GWAS:Vitamin D levels]
normal
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rs3135388 is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure sufficient vitamin D production, presumably through sunlight exposure, during as yet unknown critical periods in development. As...
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Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Vitamin d pathway genes, diet, and risk of renal cell carcinoma.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
36 snps
(hide) Weight management
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
normal
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-1 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
4 snps
(hide) Yasko Methylation
usually the ACE ALU insertion
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A and G alleles of rs4343 are strongly associated marking insertion and deletion alleles of ACE I/D respectively. For those looking for the ACE Alu Insertion/Deletion, this is a very good substitute for people searching for ACE Del16. G would mean deletion. A haplotype of rs4311, rs4343, rs699 increases risk of diabetic nephropathy 4x. [PharmGKB:Curated While the ACE:I/D has dbSNP identifiers rs1799752, rs4340, rs13447447 and rs4646994, measurement of a single base at these positions does not give an informative genotype. In Europeans, rs4343 is in complete LD with the ACE:I/D, with the A and G alleles of rs4343 marking the insertion and deletion alleles of ACE:I/D respectively.] [GWAS:Angiotensin-converting enzyme activity]
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pancreatic cancer 702 cases and 785 controls *rs162049 P = .0018; OR, 1.33; 95% CI: 1.11-1.60 *rs10380 (His595Tyr) P = .0063; OR, 1.45; 95% CI: 1.11-1.88
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No association of single nucleotide polymorphisms in one-carbon metabolism genes with prostate cancer risk. Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma.
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The GG (Gly/Gly) genotype was associated with lower risk for colorectal cancer. This risk was further lowered in men with low alcohol intake. Study size: Study population/ethnicity: Patients with colorectal cancer from the Physicians' Health Study (PHS) and the Health Professional Follow-up Study (HPFS). Significance metric(s): OR = 0.59 (95% CI, 0.27-1.27); OR = 0.27 (95% CI, 0.09-0.81)(interaction with alcohol) Type of association: CO]
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Being investigated in Ehlers-Danlos syndrome
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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Yasko Methylation Necessary to regenerate Methyl-B12 for use by MTR. Mutation can cause shortage, suggesting a need for more B12.
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower enzymatic activity *rs4680(G) = Warrior. Val, less exploratory, higher enzymatic activity Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compared with those with the Met substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may hav...
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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rs6323 (R297R / Arg297Arg) is a SNP in the MAOA (monoamine oxidase A) gene. Monoamine oxidase A degrades serotonin, dopamine, epineprine, and norepinephrine. The G allele encodes for the higher activity form of the enzyme. Subjects with major depressive disorder with the highest activity form of the enzyme (G or G/G) had a significantly lower magnitude of placebo response.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations.
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Yasko Methylation Necessary to regenerate Methyl-B12 for use by MTR. Mutation can cause shortage, suggesting a need for more B12.
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The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Influence and interaction of genetic polymorphisms in catecholamine neurotransmitter systems and early life stress on antidepressant drug response.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations.
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Being investigated in Ehlers-Danlos syndrome
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
common in clinvar
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer * cleft lip and cleft palate * coronary artery disease * depression * hyperhomocysteinemia * migraine * neural tube defects * pre-eclampsia (ges...
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Plays a major role in ketone body metabolism. Defects cause a 3-ketothiolase deficiency. Yasko believes it will cause an increase in gut bugs (particularly clostridia) as well as elevated fatty acid metabolites.
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Associated with lean body mass but not fat body mass in a study of ~1,800 Caucasians
27 snps