What this means

HERC2 contains a regulatory element that controls expression of the neighbouring OCP2 gene, which in turn regulates melanin production in the iris. The rs12913832 variant sits in that regulator: the G allele reduces OCP2 expression, lowering iris melanin and producing blue eyes. This is one of the highest-effect-size common SNPs in human genetics — about 74% of the variation in human eye colour in European populations traces back to this single position. Other genes (OCP2, SLC24A4, TYR) fill in the remaining green, hazel, and amber tones.

A single DNA change near the HERC2 gene controls how much pigment your eyes make. The "G" version turns the pigment down — that's why blue eyes happen. This one spot explains about three quarters of why some people end up with blue eyes and others with brown, at least among people of European ancestry. Other genes fill in the green, hazel, and amber shades in between.

Caveats

• Eye colour is also shaped by OCP2, SLC24A4, and TYR — this is the biggest single contributor, not the only one.
• The brown-vs-blue contrast is the cleanest signal; green and hazel are harder to predict.
• Infant eye colour can shift over the first year or two.
• This SNP is most predictive in European-ancestry populations; in populations with low blue-eye frequency the test tells you less.

References

• Eiberg et al. — Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene (Human Genetics, 2008)
• Sturm et al. — A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color (AJHG, 2008)