SNPwatch: Researchers Identify Genetic Variation That Contributes to Skin Color Differences in East Asians


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From rich brown to almost translucent white, human skin colors span a remarkable spectrum.

The evolutionary story of how we came to be such a varied species skin color-wise began around 40,000 years ago when the human groups that had left Africa and spread out along the southern coast of Asia began to move north.  When people lived near the equator, greater concentrations of the pigment melanin in their skin, hair and eyes acted as a natural sunblock to protect them from high levels of cancer-causing ultraviolet radiation. But melanin also reduces the body’s production of vitamin D, which is stimulated by ultraviolet radiation. At higher latitudes, where vitamin D deficiency is more of a survival issue than skin cancer, genetic changes that reduced melanin production were favored by natural selection.

Although the overall theory of how non-African populations came to lose some of their color is pretty well accepted, there is still a lot to learn about the details.  Much of the research has focused on European populations.  Now a new study, published recently in the journal PLoS Genetics, has identified a DNA variant involved in pigmentation that is specific to East Asian populations.

Scientists led by Esteban Parra of the University of Toronto focused their search for determinants of different shades of East Asian skin color on 10 SNPs in five genes already known to be involved in pigmentation.  They analyzed the DNA of 122 people with East Asian ancestry living in Canada, and combined the genetic information with quantitative measurements of skin color.

The scientists found that each copy of the C version of rs1800414 was associated with a 1.3 melanin unit reduction in skin pigmentation.  Although this is a small difference (variations associated with pigmentation identified in other populations have had effects of around 3 melanin units per copy), the researchers calculate that this SNP accounts for 9% of the variation in skin color seen in the study population.

(23andMe Complete Edition customer can check their data for rs1800414 using the Browse Raw Data feature.)

The researchers replicated their finding of an association of rs1800414 with skin pigmentation in a group of 207 Han Chinese people living in China, although the effect of the variation, and the percent of the variability in skin color explained, was somewhat smaller.

Genetic evidence has previously suggested that the transition from melanin-rich to melanin-poor skin took place independently in the groups that would eventually become the populations we now call European and East Asian.  The current study further supports this idea of “convergent evolution.”  Rs1800414 is in OCA2, a gene that has also been associated with pigmentation in European populations.  The variations associated with lighter skin in Europeans are not found in East Asians, however, and the C version of rs1800414 has not been found in Europeans.

Further research in diverse groups will be needed to understand exactly how human pigmentation has evolved around the world, and when in our history these changes took place.

SNPwatch gives you the latest news about research linking various traits and conditions to individual genetic variations. These studies are exciting because they offer a glimpse into how genetics may affect our bodies and health; but in most cases, more work is needed before this research can provide information of value to individuals. For that reason it is important to remember that like all information we provide, the studies we describe in SNPwatch are for research and educational purposes only. SNPwatch is not intended to be a substitute for professional medical advice; you should always seek the advice of your physician or other appropriate healthcare professional with any questions you may have regarding diagnosis, cure, treatment or prevention of any disease or other medical condition.






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  • Evelyn Khelama

    Then how do you account for the fact that East Asians and Caucasians are at greater risk for Vitamin D deficiency, and all its related bone degeneration, despite melanin reduction, than their darker melanin dominant kin? Black humans have greater bone density and higher levels of Vitamin D than white or near white humans. It is not melanin that causes reduction of Vitamin D nor is Vitamin D deficiency the reason East Asians and Caucasians are pale skinned. Take off the color blinders. I cover the real reason in an upcoming book. Stay tuned.

  • cynthia

    hi, in my family we have this genetic skin of spots like 4 color variation in which a kid develops it at around the age of 5. though our family can tell those who will develop it cos a birthmark in the stomach. none is sick or having any ailment at all. we are African but just out of curiosity would like to know what this is. searched for as long as i can but no results. i have never seen it anywhere. can trace the genetic skin to about 6 generations though. any one got any idea? can someone please assist cos n one really knows anything about it.

    • http://23andme.com Shwu

      Hi Cynthia,

      That’s very interesting! It’s possible a condition called vitiligo (vitt-eh-LIE-go) runs in your family, or it could be a similar condition related to pigmentation but caused by genetics unique to your family. You can learn more about vitiligo here: http://www.mayoclinic.com/health/vitiligo/DS00586

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