Frequencies for blue eyes SNP rs12913832 in HGDP populations

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.

rs12913832-a

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.

rs12913832-gt

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
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4 comments on “Frequencies for blue eyes SNP rs12913832 in HGDP populations
  1. genetiker says:

    Thanks for reminding me.

  2. […] comment on my post about rs12913832 pointed out that one can get allele frequencies for that SNP here, on the ALFRED site. I had […]

  3. […] June 1: Frequencies for blue eyes SNP rs12913832 in HGDP populations […]

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