Rs12913832

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Orientationplus
Geno Mag Summary
(A;A) 0 brown eye color, 80% of the time
(A;G) brown eye color
(G;G) 2 blue eye color, 99% of the time
ReferenceGRCh38 38.1/141
Chromosome15
Position28120472
GeneHERC2
is asnp
is mentioned by
dbSNPrs12913832
Exacrs12913832
PheGenIrs12913832
nextbiors12913832
hapmaprs12913832
1000 genomesrs12913832
hgdprs12913832
ensemblrs12913832
gopubmedrs12913832
geneviewrs12913832
scholarrs12913832
googlers12913832
pharmgkbrs12913832
gwascentralrs12913832
openSNPrs12913832
23andMers12913832
23andMe allrs12913832
SNP Nexus

SNPshotrs12913832
SNPdbers12913832
MSV3drs12913832
GMAF0.2911
? (A;A) (A;G) (G;G) 28
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.[PMID 18172690, PMID 18252222]

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). 10.1371/journal.pgen.1000993rs12913832 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.[PMID 18172690]

[PMID 18650849] rs12913832-T (brown eye) homozygotes compared to rs12913832-C (blue eye). correlations with skin, eye, and hair color variation.

The "h-1" haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows [PMID 18172690]:

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)

blog coverage

Neighborrs7183877
Distance115
GWAS
SNP rs12913832
PubMedID [PMID 18483556OA-icon.png]
Condition Black vs. red hair color
Gene HERC2
Risk Allele A
pValue 1.00E-077
OR 0.44
95% CI 0.40-0.48) decrease in hair color scor


[PMID 19278018] Brief communication: Blue eyes in lemurs and humans: Same phenotype, different genetic mechanism

[PMID 19208107] Interactions between HERC2, OCA2 and MC1R may influence human pigmentation phenotype.

OMIM227220
DescSKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 1; SHEP1
Variant
Relatedalso
OMIM605837
DescHECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2
Variant
Relatedalso
OMIM611409
DescOCA2 GENE
Variant
Relatedalso


GWAS snp
PMID [PMID 20463881OA-icon.png]
Trait Eye color traits
Title Digital quantification of human eye color highlights genetic association of three new loci
Risk Allele
P-val 0
Odds Ratio None None
GWAS snp
PMID [PMID 20585627OA-icon.png]
Trait Eye color
Title Web-based, participant-driven studies yield novel genetic associations for common traits
Risk Allele A
P-val 3E-52
Odds Ratio 8.43 [NR]


[PMID 20457063] Human eye colour and HERC2, OCA2 and MATP

OMIM605837
Desc
Variant0003
Relatedalso
[PMID 22615734OA-icon.png] The Classical Pink-Eyed Dilution Mutation Affects Angiogenic Responsiveness


[PMID 22234890OA-icon.png] HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter.


[PMID 19340012OA-icon.png] Genome-wide association study of tanning phenotype in a population of European ancestry.


[PMID 19472299] Genotyping of five single nucleotide polymorphisms in the OCA2 and HERC2 genes associated with blue-brown eye color in the Japanese population.


[PMID 19619260] Genetics of human iris colour and patterns.


[PMID 19668368OA-icon.png] Ancestry analysis in the 11-M Madrid bomb attack investigation.


[PMID 19711812] [Genetic analysis of the putative remains of general Wladyslaw Sikorski].


[PMID 20018053OA-icon.png] A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests.


[PMID 20221248OA-icon.png] Association of the OCA2 polymorphism His615Arg with melanin content in east Asian populations: further evidence of convergent evolution of skin pigmentation.


[PMID 20569440OA-icon.png] Alterations in LMTK2, MSMB and HNF1B gene expression are associated with the development of prostate cancer.


[PMID 20629734] Genetic analysis of three important genes in pigmentation and melanoma susceptibility: CDKN2A, MC1R and HERC2/OCA2.


[PMID 21253569OA-icon.png] Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations?


[PMID 21926416OA-icon.png] Genome-wide association study identifies novel loci predisposing to cutaneous melanoma.


[PMID 22101828] Technical note: quantitative measures of iris color using high resolution photographs.


GET Evidence
rs12913832
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.289062
summary



[PMID 23100201OA-icon.png] A single-nucleotide polymorphism (SNP) multiplex system: the association of five SNPs with human eye and hair color in the Slovenian population and comparison using a Bayesian network and logistic regression model


[PMID 23548203OA-icon.png] Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans


[PMID 22709892] Further development of forensic eye color predictive tests.


[PMID 23543094OA-icon.png] Testing for associations between loci and environmental gradients using latent factor mixed models.


[PMID 23771755OA-icon.png] Improved eye- and skin-color prediction based on 8 SNPs.