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However, how genomic variations affect skin pigmentation and how these skin pigmentation gene variants affect serum 25(OH) vitamin D variation has not been explored in African Americans (AAs). In order to further understand genetic factors that affect human skin pigmentation and serum 25(OH)D variation, we performed a GWAS for skin pigmentation with 395 AAs and a replication study with 681 AAs. Then, we tested if the identified variants are associated with serum 25(OH) D concentrations in a subset of AAs (n = 591). Skin pigmentation, Melanin Index (M-Index), was measured using a narrow-band reflectometer. Multiple regression analysis was performed to identify variants associated with M-Index and to assess their role in serum 25(OH)D variation adjusting for population stratification and relevant confounding variables. A variant near the<jats:italic>SLC24A5<\/jats:italic>gene (rs2675345) showed the strongest signal of association with M-Index (<jats:italic>P<\/jats:italic>= 4.0 x 10<jats:sup>\u221230<\/jats:sup>in the pooled dataset). Variants in<jats:italic>SLC24A5<\/jats:italic>,<jats:italic>SLC45A2<\/jats:italic>and<jats:italic>OCA2<\/jats:italic>together account for a large proportion of skin pigmentation variance (11%). The effects of these variants on M-Index was modified by sex (<jats:italic>P<\/jats:italic>for interaction = 0.009). However, West African Ancestry (WAA) also accounts for a large proportion of M-Index variance (23%). M-Index also varies among AAs with high WAA and high Genetic Score calculated from top variants associated with M-Index, suggesting that other unknown genomic factors related to WAA are likely contributing to skin pigmentation variation. M-Index was not associated with serum 25(OH)D concentrations, but the Genetic Score was significantly associated with vitamin D deficiency (serum 25(OH)D levels less than 12 ng\/mL) (OR, 1.30; 95% CI, 1.04\u20131.64). The findings support the hypothesis suggesting that skin pigmentation evolved responding to increased demand for subcutaneous vitamin D synthesis in high latitude environments.<\/jats:p>","DOI":"10.1371\/journal.pgen.1009319","type":"journal-article","created":{"date-parts":[[2021,2,18]],"date-time":"2021-02-18T18:35:06Z","timestamp":1613673306000},"page":"e1009319","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":28,"title":["Genetic loci associated with skin pigmentation in African Americans and their effects on vitamin D deficiency"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0317-1118","authenticated-orcid":true,"given":"Ken","family":"Batai","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3962-7711","authenticated-orcid":true,"given":"Zuxi","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit","family":"Arora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ebony","family":"Shah-Williams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenndy","family":"Hernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8931-3879","authenticated-orcid":true,"given":"Maria","family":"Ruden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9152-4106","authenticated-orcid":true,"given":"Courtney M. P.","family":"Hollowell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8680-4856","authenticated-orcid":true,"given":"Stanley E.","family":"Hooker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madhavi","family":"Bathina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9977-3473","authenticated-orcid":true,"given":"Adam B.","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9972-6383","authenticated-orcid":true,"given":"Carolina","family":"Bonilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5004-4437","authenticated-orcid":true,"given":"Rick A.","family":"Kittles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,2,18]]},"reference":[{"key":"pgen.1009319.ref001","doi-asserted-by":"crossref","first-page":"e1000993","DOI":"10.1371\/journal.pgen.1000993","article-title":"Web-based, participant-driven studies yield novel genetic associations for common traits.","volume":"6","author":"N Eriksson","year":"2010","journal-title":"PLoS Genet"},{"issue":"6","key":"pgen.1009319.ref002","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1086\/522235","article-title":"A genomewide association study of skin pigmentation in a South Asian population","volume":"81","author":"RP Stokowski","year":"2007","journal-title":"Am J Hum Genet"},{"issue":"7","key":"pgen.1009319.ref003","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/ng.160","article-title":"Two newly identified genetic determinants of pigmentation in Europeans","volume":"40","author":"P Sulem","year":"2008","journal-title":"Nat Genet"},{"issue":"9","key":"pgen.1009319.ref004","doi-asserted-by":"crossref","first-page":"2250","DOI":"10.1038\/jid.2009.62","article-title":"Genome-Wide Association Study of Tanning Phenotype in a Population of European Ancestry","volume":"129","author":"H Nan","year":"2009","journal-title":"J Invest Dermatol"},{"key":"pgen.1009319.ref005","doi-asserted-by":"crossref","first-page":"e1000074","DOI":"10.1371\/journal.pgen.1000074","article-title":"A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation.","volume":"4","author":"J Han","year":"2008","journal-title":"PLoS Genet"},{"issue":"1","key":"pgen.1009319.ref006","doi-asserted-by":"crossref","first-page":"5271","DOI":"10.1038\/s41467-018-07691-z","article-title":"Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability.","volume":"9","author":"MD Morgan","year":"2018","journal-title":"Nat Commun."},{"issue":"1","key":"pgen.1009319.ref007","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/s41467-018-08147-0","article-title":"A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia.","volume":"10","author":"K Adhikari","year":"2019","journal-title":"Nat Commun"},{"issue":"6365","key":"pgen.1009319.ref008","doi-asserted-by":"crossref","DOI":"10.1126\/science.aan8433","article-title":"Loci associated with skin pigmentation identified in African populations","volume":"358","author":"NG Crawford","year":"2017","journal-title":"Science"},{"issue":"6","key":"pgen.1009319.ref009","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1016\/j.cell.2017.11.015","article-title":"An unexpectedly complex architecture for skin pigmentation in Africans","volume":"171","author":"AR Martin","year":"2017","journal-title":"Cell"},{"issue":"1","key":"pgen.1009319.ref010","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s12863-019-0765-5","article-title":"Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations","volume":"20","author":"F Lona-Durazo","year":"2019","journal-title":"BMC Genet"},{"issue":"1724","key":"pgen.1009319.ref011","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2016.0349","article-title":"The colours of humanity: the evolution of pigmentation in the human lineage","volume":"372","author":"NG Jablonski","year":"2017","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"pgen.1009319.ref012","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1353\/pbm.1988.0010","article-title":"Human skin color: a possible relationship between its sexual dimorphism and its social perception.","volume":"32","author":"P. 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