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A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation
Open accessAbstract
We have previously shown that a quantitative-trait locus linked to the OCA2 region of 15q accounts for 74% of variation in human eye color. We conducted additional genotyping to clarify the role of the OCA2 locus in the inheritance of eye color and other pigmentary traits associated with skin-cancer risk in white populations. Fifty-eight synonymous and nonsynonymous exonic single-nucleotide polymorphisms (SNPs) and tagging SNPs were typed in a collection of 3,839 adolescent twins, their siblings, and their parents. The highest association for blue/nonblue eye color was found with three OCA2 SNPs: rs7495174 T/C, rs6497268 G/T, and rs11855019 T/C (P values of 1.02x10(-61), 1.57x10(-96), and 4.45x10(-54), respectively) in intron 1. These three SNPs are in one major haplotype block, with TGT representing 78.4% of alleles. The TGT/TGT diplotype found in 62.2% of samples was the major genotype seen to modify eye color, with a frequency of 0.905 in blue or green compared with only 0.095 in brown eye color. This genotype was also at highest frequency in subjects with light brown hair and was more frequent in fair and medium skin types, consistent with the TGT haplotype acting as a recessive modifier of lighter pigmentary phenotypes. Homozygotes for rs11855019 C/C were predominantly without freckles and had lower mole counts. The minor population impact of the nonsynonymous coding-region polymorphisms Arg305Trp and Arg419Gln associated with nonblue eyes and the tight linkage of the major TGT haplotype within the intron 1 of OCA2 with blue eye color and lighter hair and skin tones suggest that differences within the 5' proximal regulatory control region of the OCA2 gene alter expression or messenger RNA-transcript levels and may be responsible for these associations.
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In the citing paper
“Normal polymorphism of OCA2 appears to be predominantly associated with eye color, although effects on skin and hair color have also been reported”
From Analysis of Cultured Human Melanocytes Based on Polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P Loci (2009) · cites this paper as Duffy et al., 2007
In the citing paper
“Duffy et al. (2007) previously identified a three-SNP haplotype system (rs4778138, rs4778241, and rs7495174) associated with blue eyes; for the purpose of this paper, we will refer to this system as BEH1, blue-eye associated haplotype #1.”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007
In the citing paper
“Several sites in and around OCA2 have been reported to be the functional variant or to be tightly linked to the functional variant leading to blue eyes. These sites include a three-SNP haplotype (rs4778138, rs4778241, rs7495174) and four individual SNPs, rs1129038, rs12913832, rs916977, and rs1667394 (Duffy et al. 2007; Sturm et al. 2008; Kayser et al. 2008; Sulem et al. 2007; Mengel-From et al. 2”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007
In the citing paper
“In humans, it has been implicated in iris, skin, and hair pigmentation (Duffy et al. 2007; Sturm et al. 2008; Kayser et al. 2008; Sulem et al. 2007).”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007
In the citing paper
“We have shown that the TG allele of BEH2 has a much more restricted global distribution compared to the ACA allele of BEH1 and the CA allele of BEH3, the other two haplotypes published as associated with blue eyes”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007
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Metadata
- Authors
- Duffy, D. L., Montgomery, G. W., Chen, W., Zhao, Z. Z., Le, L., James, M. R., Hayward, N. K., Martin, N. G., & Sturm, R. A.
- Affiliations
- QIMR Berghofer Medical Research Institute (AU)
- The University of Queensland (AU)
- Corresponding author
- Sturm, Richard A.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2007-02
- Volume
- 80
- Issue
- 2
- Pages
- 241-252
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC1785344
- OpenAlex
- W2014370194
- Cited by
- 240
- References
- 64
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 14 · 2023: 8 · 2022: 8 · 2021: 15 · 2020: 12 · 2019: 8 · 2018: 8 · 2017: 5 · 2016: 8 · 2015: 10 · 2014: 10 · 2013: 15 · 2012: 15
- FWCI
- 11.17
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Medical Research Council
- Australian Research Council (241944, 389875)
- National Health and Medical Research Council (301173, 241944, 389875)
- National Cancer Institute (R01CA088363, CA88363)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- OCA2, eye color, single nucleotide polymorphisms, haplotypes, intron 1, skin pigmentation, hair color, freckles, skin cancer risk, quantitative trait loci
- MeSH terms
- Adolescent, Child, Chromosomes, Human, Pair 15, Eye Color, Female, Genotype, Hair Color, Haplotypes, Humans, Introns, Male, Melanosis, Nevus, Pigmented, Skin Pigmentation, Twins, Polymorphism, Single Nucleotide, Membrane Transport Proteins
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