OBJECTIVES: South Asians exhibit extensive variation in skin melanin index (MI) 
which is observed across the broader region of South Asia as well as within 
restricted geographic regions. However, the genetic variants associated with 
variation in the skin pigmentation phenotype are poorly understood in these 
populations. The present study examines the association between MI measures and 
genetic variants from 5 candidate pigmentation genes among 533 individuals 
representing 6 populations of West Maharashtra.
METHODS: Associations between five single nucleotide polymorphisms (SNPs) known 
to play a role in pigmentation (rs1426654-SLC24A5, rs1042602-TYR, 
rs16891982-SLC45A2, rs6058017-ASIP, and rs642742-KITLG) and MI measures were 
tested using standard one-way analysis of variance (ANOVA) within each 
population. Multiple linear regression was used to test the effects of these 
SNPs in the full West Maharashtra sample using sex, age, and population or 
social group as covariates.
RESULTS: rs1426654 showed significant association with MI in all six study 
populations (P < 0.01). Association tests using sex, age, and population as 
covariates showed rs1426654 and rs1042602 to be significantly (P < 0.01) 
associated with lighter skin pigmentation in West Maharashtra as a whole. By 
contrast, when social group was added as a covariate instead of population, 
rs1426654, rs1042602, and rs16891982 were significantly (P < 0.01) associated 
with lighter skin pigmentation.
CONCLUSIONS: Only rs1426654 is significantly associated with MI in each 
individual population; however, rs1426654, rs1042602, and rs16891982 are 
significantly associated with pigmentation in the broader West Maharashtra 
region after controlling for population and social group, with rs1426654 
(SLC24A5) explaining the majority of the observed variation. Am. J. Hum. Biol. 
28:610-618, 2016. © 2016 Wiley Periodicals, Inc.