A genomewide association study of skin pigmentation in a South Asian population

Am J Hum Genet. 2007 Dec;81(6):1119-32. doi: 10.1086/522235. Epub 2007 Oct 15.


We have conducted a multistage genomewide association study, using 1,620,742 single-nucleotide polymorphisms to systematically investigate the genetic factors influencing intrinsic skin pigmentation in a population of South Asian descent. Polymorphisms in three genes--SLC24A5, TYR, and SLC45A2--yielded highly significant replicated associations with skin-reflectance measurements, an indirect measure of melanin content in the skin. The associations detected in these three genes, in an additive manner, collectively account for a large fraction of the natural variation of skin pigmentation in a South Asian population. Our study is the first to interrogate polymorphisms across the genome, to find genetic determinants of the natural variation of skin pigmentation within a human population.

MeSH terms

  • Antigens, Neoplasm / genetics*
  • Antiporters / genetics*
  • Bangladesh
  • Gene Frequency
  • Genome, Human*
  • Humans
  • India
  • Melanins / analysis*
  • Membrane Transport Proteins / genetics*
  • Pakistan
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • Skin Physiological Phenomena*
  • Skin Pigmentation / genetics*
  • Sri Lanka


  • Antigens, Neoplasm
  • Antiporters
  • Melanins
  • Membrane Transport Proteins
  • SLC24A5 protein, human
  • SLC45A2 protein, human