biostudies-literatureHernandez-Pacheco NNIEHS NIH HHSNHLBI NIH HHSNIMHD NIH HHSNIGMS NIH HHS44548https://www.ebi.ac.uk/biostudies/studies/S-EPMC5353593biostudies-literatureUnknown7Skin 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.Scientific reportsIdentification of a novel locus associated with skin colour in African-admixed populations.PMC5353593R01 MD010443R01 HL117004R21 ES024844R01 ES015794K12 GM081266R01 HL128439P60 MD006902Lenoir MPino-Yanes MAlonso SBurchard EGSerebrisky DRodriguez-Santana JRMak ACFarber HJFlores CMeade KRodriguez-Cintron WOh SSSen SKumar RBrigino-Buenaventura EHu DHernandez-Pacheco NHunstman SWhite MJAvila PCEng CThyne SMfalseIdentification of a novel locus associated with skin colour in African-admixed populations.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.2017-01-01T00:00:00Z2017 Mar2024-12-03T22:30:19.558Z2019-03-27T02:38:45ZS-EPMC53535932830020110.1038/srep44548