Skip to main content
Open Access Publications from the University of California


UC San Francisco Previously Published Works bannerUCSF

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

  • Author(s): Hernandez-Pacheco, Natalia;
  • Flores, Carlos;
  • Alonso, Santos;
  • Eng, Celeste;
  • Mak, Angel CY;
  • Hunstman, Scott;
  • Hu, Donglei;
  • White, Marquitta J;
  • Oh, Sam S;
  • Meade, Kelley;
  • Farber, Harold J;
  • Avila, Pedro C;
  • Serebrisky, Denise;
  • Thyne, Shannon M;
  • Brigino-Buenaventura, Emerita;
  • Rodriguez-Cintron, William;
  • Sen, Saunak;
  • Kumar, Rajesh;
  • Lenoir, Michael;
  • Rodriguez-Santana, Jose R;
  • Burchard, Esteban G;
  • Pino-Yanes, Maria
  • et al.

Published Web Location

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.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
For improved accessibility of PDF content, download the file to your device.
Current View