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J Invest Dermatol. 2017 Mar;137(3):670-677. doi: 10.1016/j.jid.2016.10.043. Epub 2016 Nov 17.

Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation.

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CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia.
Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India.
Department of Biotechnology, V.B.S. Purvanchal University, Jaunpur, India.
Estonian Biocentre, Tartu, Estonia; Insitute of Mathematical Statistics, University of Tartu, Tartu, Estonia.
Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA.
Department of Anthropology, Delhi University, New Delhi, India.
Oriental Institute of Science and Technology, Bhopal, India.
Estonian Biocentre, Tartu, Estonia.
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India. Electronic address:


Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.

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