Identification of a novel locus associated with skin colour in African-admixed populations

Sci Rep. 2017 Mar 16:7:44548. doi: 10.1038/srep44548.


Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10-5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10-14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10-10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10-9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, Neoplasm / genetics*
  • Antiporters / genetics*
  • Asian People / genetics
  • Black or African American / genetics
  • DNA, Intergenic / genetics*
  • Female
  • Genetic Loci*
  • Genome-Wide Association Study
  • Genotype
  • Hispanic or Latino / genetics
  • Humans
  • Male
  • Membrane Transport Proteins / genetics*
  • Phenotype
  • Polymorphism, Single Nucleotide / genetics
  • Proteins / genetics*
  • RNA Splicing Factors / genetics*
  • Skin Pigmentation / genetics*
  • Skin Pigmentation / physiology
  • White People / genetics


  • Antigens, Neoplasm
  • Antiporters
  • BEND7 protein, human
  • DNA, Intergenic
  • Membrane Transport Proteins
  • PRPF18 protein, human
  • Proteins
  • RNA Splicing Factors
  • SLC24A5 protein, human
  • SLC45A2 protein, human