rs12913832

plus

Geno	Mag	Summary
(A;A)	0	brown eye color, 80% of the time
(A;G)		brown eye color
(G;G)	2.5	blue eye color, 99% of the time

Reference

GRCh38 38.1/141

Chromosome

15

Position

28120472

Gene

HERC2

is a	snp
is	mentioned by
dbSNP	rs12913832
dbSNP (classic)	rs12913832
ClinGen	rs12913832
ebi	rs12913832
HLI	rs12913832
Exac	rs12913832
Gnomad	rs12913832
Varsome	rs12913832
LitVar	rs12913832
Map	rs12913832
PheGenI	rs12913832
Biobank	rs12913832
1000 genomes	rs12913832
hgdp	rs12913832
ensembl	rs12913832
geneview	rs12913832
scholar	rs12913832
google	rs12913832
pharmgkb	rs12913832
gwascentral	rs12913832
openSNP	rs12913832
23andMe	rs12913832
SNPshot	rs12913832
SNPdbe	rs12913832
MSV3d	rs12913832
GWAS Ctlg	rs12913832

GMAF

0.2911

Max Magnitude

2.5

?

(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.1000993

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.[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

10.1038/ncomms10815 A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

GWAS
SNP	rs12913832
PubMedID	[PMID 18483556 ]
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.

OMIM	227220
Desc	SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 1; SHEP1
Variant
Related	also

OMIM	605837
Desc	HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2
Variant
Related	also

OMIM	611409
Desc	OCA2 GENE
Variant
Related	also

GWAS snp
PMID	[PMID 20463881 ]
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 20585627 ]
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

OMIM	605837
Desc
Variant	0003
Related	also

[PMID 22615734 ] The Classical Pink-Eyed Dilution Mutation Affects Angiogenic Responsiveness

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

[PMID 19340012 ] 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 19668368 ] Ancestry analysis in the 11-M Madrid bomb attack investigation.

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

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

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

[PMID 20569440 ] 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 21253569 ] Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations?

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

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

[PMID 23100201 ] 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 23548203 ] 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 23543094 ] Testing for associations between loci and environmental gradients using latent factor mixed models.

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

ClinVar
Risk	Rs12913832(G;G)
Alt	Rs12913832(G;G)
Reference	Rs12913832(A;A)
Significance	Other
Disease	Skin/hair/eye pigmentation
Variation	info
Gene	HERC2
CLNDBN	Skin/hair/eye pigmentation, variation in, 1
Reversed	0
HGVS	NC_000015.9:g.28365618A>G
CLNSRC	OMIM Allelic Variant
CLNACC	RCV000005011.3,

[PMID 28242083] Association of five SNPs with human hair colour in the Polish population.