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Background  Association studies in recently admixed populations are extremely useful to identify the genetic architecture of pigmentation, due to their high genotypic and phenotypic variation. However, to date only four Genome-Wide Association Studies (GWAS) have been carried out in these populations.    Results  We present a GWAS of skin pigmentation in an admixed sample from Cuba ( N  = 762). Additionally, we conducted a meta-analysis including the Cuban sample, and admixed samples from Cape Verde, Puerto Rico and African-Americans from San Francisco. This meta-analysis is one of the largest efforts so far to characterize the genetic basis of skin pigmentation in admixed populations ( N  = 2,104). We identified five genome-wide significant regions in the meta-analysis, and explored if the markers observed in these regions are associated with the expression of relevant pigmentary genes in human melanocyte cultures. In three of the regions identified in the meta-analysis ( SLC24A5 ,  SLC45A2,  and  GRM5/TYR ), the association seems to be driven by non-synonymous variants (rs1426654, rs16891982, and rs1042602, respectively). The rs16891982 polymorphism is strongly associated with the expression of the  SLC45A2  gene. In the  GRM5/TYR  region, in addition to the rs1042602 non-synonymous SNP located on the  TYR  gene, variants located in the nearby  GRM5  gene have an independent effect on pigmentation, possibly through regulation of gene expression of the  TYR  gene. We also replicated an association recently described near the  MFSD12  gene on chromosome 19 (lead variant rs112332856). Additionally, our analyses support the presence of multiple signals in the  OCA2/HERC2/APBA2  region on chromosome 15. A clear causal candidate is the  HERC2  intronic variant rs12913832, which has a profound influence on  OCA2  expression. This variant has pleiotropic effects on eye, hair, and skin pigmentation. However, conditional and haplotype-based analyses indicate the presence of other variants with independent effects on melanin levels in  OCA2  and  APBA2 . Finally, a follow-up of genome-wide signals identified in a recent GWAS for tanning response indicates that there is a substantial overlap in the genetic factors influencing skin pigmentation and tanning response.    Conclusions  Our meta-analysis of skin pigmentation GWAS in recently admixed populations provides new insights about the genetic architecture of this complex trait.    Electronic supplementary material  The online version of this article (10.1186/s12863-019-0765-5) contains supplementary material, which is available to authorized users.

Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations