Study finds new genes that affect hair, eye and skin colour.

Scientists at deCODE genetics and colleagues in Iceland and Holland have reported the discovery of variations in the human genome that influence pigmentation of hair, eyes and skin.  By studying more than 300,000 SNPs (single-letter variants in the human genome) across the whole genome in close to seven thousand individuals of European origin, the deCODE team discovered several novel SNPs influencing hair, eye, and skin pigmentation, at the same time refining earlier findings influencing these traits.
The findings help in the understanding of the molecular basis for and evolution of these most visible of characteristics, and may be useful for teasing out the biology of skin and eye disease as well as for forensic DNA analysis. The paper, entitled “Genetic determinants of hair, eye and skin pigmentation in Europeans,” has been published online in Nature Genetics.
It is known that pigmentation characteristics such as freckles and hair and eye colour run in families. However, only few genes have been strongly linked to normal variation of these characteristics. Skin pigmentation in human populations tends to be darkest near the equator and to lighten with increasing latitude. This variation has a generally accepted dual biological function: heavier pigmentation affords protection against ultraviolet radiation in sunlight, protecting against sunburn and skin cancer but also reduces the body’s capacity to synthesize vitamin D. By contrast, there is no clear functional role for hair and eye color. The vast majority of variations in these two traits is confined to populations of European origin, with most populations around the globe with only dark hair and brown eyes.
Most of the novel variants presented in this study demonstrate signs of positive evolutionary selection in people of European origin, and those contributing to lighter pigmentation of the skin appear to have been under the strongest selective pressure. Intriguingly, some variants contribute to variation in just one trait; others to two or three. Among the findings of the deCODE group is a SNP on chromosome 14 in the SLC24A4 gene that is associated with increased likelihood of blond as opposed to brown hair and blue as opposed to green eyes. A SNP on chromosome 6p25 is associated with an increased likelihood of freckles and skin sensitivity to sunlight, as well as to brown hair. A sequence variant near the KITLG gene on chromosome 12 is associated with an increased likelihood of having blond rather than brown hair. One SNP in the tyrosinase gene is associated with freckling, and another associates with the likelihood of having blue as opposed to green eyes, as well as to skin sensitivity to sunlight.
The deCODE team has also provided detailed support for the previously reported association in the MC1R gene with red hair, freckling and skin sensitivity to sun. Similarly, the well known association of variants near the OCA2 gene with eye and hair colour, was replicated but also substantially refined. Taken together, the variants described in this report enable prediction of pigmentation traits based upon an individual’s DNA.
According to deCode, this study has significantly improved the accuracy of predicting green eyes (SLC24A4, TYR), hair shade (SLC24A4, TYR, KITLG) and freckling (TYR, 6p25). Some of the novel association patterns differ in unexpected ways from previous findings. The variant in SLC24A4 is important for gauging likelihood of blue versus green eyes, but, in contrast to variants in OCA2, has only marginal impact on likelihood of blue versus brown eyes. The completely novel SNP discovered on 6p25 associates with freckles and brown hair, whereas the SNPs in MC1R associate with freckles and red hair. The multitude of genes affecting pigmentation and their varied effects are reflected in the great degree of diversity of pigmentation seen in Europeans.
 We conducted a multi-stage genome-wide association study of natural hair color in more than 10,000 men and women of European ancestry from the United States and Australia. An initial analysis of 528,173 single nucleotide polymorphisms (SNPs) genotyped on 2,287 women identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. We confirmed these associations in 7,028 individuals from three additional studies. Across these four studies, SLC24A4 rs12896399 and IRF4 rs12203592 showed strong associations with hair color, with p=6.0×10−62 and p=7.46×10−127, respectively. The IRF4 SNP was also associated with skin color (p=6.2×10−14), eye color (p=6.1×10−13), and skin tanning response to sunlight (p=3.9×10−89). A multivariable analysis pooling data from the initial GWAS and an additional 1,440 individuals suggested that the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. After adjustment for rs12203592, the association between rs1540771 and hair color was not significant (p=0.52). One variant in the MATP gene was associated with hair color. A variant in the HERC2 gene upstream of the OCA2 gene showed the strongest and independent association with hair color compared with other SNPs in this region, including three previously reported SNPs. The signals detected in a region around the MC1R gene were explained by MC1R red hair color alleles. Our results suggest that the IRF4 and SLC24A4 loci are associated with human hair color and skin pigmentation.
The genetics of hair, skin and eye colour are very intertwined, and I won’t even pretend to understand the intricacies of of it.

One response to “Study finds new genes that affect hair, eye and skin colour.

  1. THis is a very interesting study. I am actually trying to write a paper about the correlation, or lack of a correlation, between hair color and personality traits. I believe that stereotypes exists for a reason, and I want to know what the genes that code for hair, eye, and skin color are coding for in our brain. We are able to determine the relationship between physical traits alot better than those between physical and mental qualities. If you have any input please let me know it owuld be greatly appreciated.

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