The SNP that is most strongly associated with blue eyes is rs12913832. It’s on chromosome 15 in intron 86 of the HERC2 gene, and two copies of its mutant G allele result in reduced expression of the nearby OCA2 gene, which in turn reduces production of melanin in the iris. There’s a lot of information about this SNP on its SNPedia page. According to that page, the AA genotype results in brown eyes 80% of the time, the AG genotype also results in brown eyes, and the GG genotype results in blue eyes 99% of the time.
I calculated the allele and genotype frequencies for rs12913832 for all of the HGDP populations. The results are below.
The G allele is present in the Karitiana at a frequency of 0.346, and 7.7% of them are homozygous for it.
The G allele is present in the Surui at a frequency of 0.188, but none of them are homozygous for it.
The G allele is present in the Maya at a frequency of 0.071, but none of them are homozygous for it.
The G allele is absent in the Colombians and the Pima.
Below is a plot of the allele frequencies. The A allele is brown and the G allele is blue.
Below is a plot of the genotype frequencies. The AA genotype is dark brown, the AG genotype is light brown, and the GG genotype is blue.
Below is a table of the allele frequencies.
A G Russian 0.1521739 0.84782609 Italian 0.3333333 0.66666667 Orcadian 0.3461538 0.65384615 French 0.3928571 0.60714286 Tuscan 0.5625000 0.43750000 Basque 0.5909091 0.40909091 Karitiana 0.6538462 0.34615385 Adygei 0.6764706 0.32352941 Druze 0.6785714 0.32142857 Burusho 0.7000000 0.30000000 Palestinian 0.7888889 0.21111111 Kalash 0.7894737 0.21052632 Pathan 0.7954545 0.20454545 Sardinian 0.8035714 0.19642857 Surui 0.8125000 0.18750000 Balochi 0.8333333 0.16666667 Bedouin 0.8913043 0.10869565 Makrani 0.9000000 0.10000000 Uygur 0.9000000 0.10000000 Mozabite 0.9074074 0.09259259 Maya 0.9285714 0.07142857 Sindhi 0.9375000 0.06250000 Hazara 0.9545455 0.04545455 Brahui 0.9583333 0.04166667 Yakut 0.9600000 0.04000000 BantuKenya 1.0000000 0.00000000 BantuSouthAfrica 1.0000000 0.00000000 BiakaPygmy 1.0000000 0.00000000 Cambodian 1.0000000 0.00000000 Colombian 1.0000000 0.00000000 Dai 1.0000000 0.00000000 Daur 1.0000000 0.00000000 Han 1.0000000 0.00000000 Han-NChina 1.0000000 0.00000000 Hezhen 1.0000000 0.00000000 Japanese 1.0000000 0.00000000 Lahu 1.0000000 0.00000000 Mandenka 1.0000000 0.00000000 MbutiPygmy 1.0000000 0.00000000 Melanesian 1.0000000 0.00000000 Miao 1.0000000 0.00000000 Mongola 1.0000000 0.00000000 Naxi 1.0000000 0.00000000 Oroqen 1.0000000 0.00000000 Papuan 1.0000000 0.00000000 Pima 1.0000000 0.00000000 San 1.0000000 0.00000000 She 1.0000000 0.00000000 Tu 1.0000000 0.00000000 Tujia 1.0000000 0.00000000 Xibo 1.0000000 0.00000000 Yi 1.0000000 0.00000000 Yoruba 1.0000000 0.00000000
Below is a table of the genotype frequencies.
AA AG GG Russian 0.00000000 0.30434783 0.69565217 Italian 0.08333333 0.50000000 0.41666667 Orcadian 0.07692308 0.53846154 0.38461538 French 0.17857143 0.42857143 0.39285714 Tuscan 0.37500000 0.37500000 0.25000000 Basque 0.40909091 0.36363636 0.22727273 Karitiana 0.38461538 0.53846154 0.07692308 Adygei 0.41176471 0.52941176 0.05882353 Druze 0.52380952 0.30952381 0.16666667 Burusho 0.44000000 0.52000000 0.04000000 Palestinian 0.60000000 0.37777778 0.02222222 Kalash 0.57894737 0.42105263 0.00000000 Pathan 0.59090909 0.40909091 0.00000000 Sardinian 0.64285714 0.32142857 0.03571429 Surui 0.62500000 0.37500000 0.00000000 Balochi 0.70833333 0.25000000 0.04166667 Bedouin 0.78260870 0.21739130 0.00000000 Makrani 0.80000000 0.20000000 0.00000000 Uygur 0.90000000 0.00000000 0.10000000 Mozabite 0.81481481 0.18518519 0.00000000 Maya 0.85714286 0.14285714 0.00000000 Sindhi 0.87500000 0.12500000 0.00000000 Hazara 0.90909091 0.09090909 0.00000000 Brahui 0.91666667 0.08333333 0.00000000 Yakut 0.92000000 0.08000000 0.00000000 BantuKenya 1.00000000 0.00000000 0.00000000 BantuSouthAfrica 1.00000000 0.00000000 0.00000000 BiakaPygmy 1.00000000 0.00000000 0.00000000 Cambodian 1.00000000 0.00000000 0.00000000 Colombian 1.00000000 0.00000000 0.00000000 Dai 1.00000000 0.00000000 0.00000000 Daur 1.00000000 0.00000000 0.00000000 Han 1.00000000 0.00000000 0.00000000 Han-NChina 1.00000000 0.00000000 0.00000000 Hezhen 1.00000000 0.00000000 0.00000000 Japanese 1.00000000 0.00000000 0.00000000 Lahu 1.00000000 0.00000000 0.00000000 Mandenka 1.00000000 0.00000000 0.00000000 MbutiPygmy 1.00000000 0.00000000 0.00000000 Melanesian 1.00000000 0.00000000 0.00000000 Miao 1.00000000 0.00000000 0.00000000 Mongola 1.00000000 0.00000000 0.00000000 Naxi 1.00000000 0.00000000 0.00000000 Oroqen 1.00000000 0.00000000 0.00000000 Papuan 1.00000000 0.00000000 0.00000000 Pima 1.00000000 0.00000000 0.00000000 San 1.00000000 0.00000000 0.00000000 She 1.00000000 0.00000000 0.00000000 Tu 1.00000000 0.00000000 0.00000000 Tujia 1.00000000 0.00000000 0.00000000 Xibo 1.00000000 0.00000000 0.00000000 Yi 1.00000000 0.00000000 0.00000000 Yoruba 1.00000000 0.00000000 0.00000000
Genetiker 
http://alfred.med.yale.edu/alfred/mvograph.asp?siteuid=SI007119S
Thanks for reminding me.
[…] comment on my post about rs12913832 pointed out that one can get allele frequencies for that SNP here, on the ALFRED site. I had […]
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