Meta-analysis and prioritization of human skin pigmentation-associated GWAS-SNPs using ENCODE data-based web-tools

  • Kausik Ganguly
  • Tania Saha
  • Arpan Saha
  • Tithi Dutta
  • Souradeep Banerjee
  • Debmalya Sengupta
  • Sreyashi Bhattacharya
  • Sampurna Ghosh
  • Mainak SenguptaEmail author
Original Paper


Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3′UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several ENCODE-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations.


Pigmentation GWAS ENCODE SNP Melanin 



The study was supported by funding from Department of Science and Technology-Promotion of University Research and Scientific Excellence (DST-PURSE), Government of India. K Ganguly is supported by Senior Research Fellowship from Council of Scientific & Industrial Research (CSIR), India, provided to Department of Genetics, University of Calcutta. T Saha and D Sengupta are supported by Senior Research Fellowship from University Grants Commission, Government of India.


This study has been partially supported by: The Department of Science and Technology (DST), Government of India, Promotion of University Research and Scientific Excellence (DST-PURSE) provided to University of Calcutta. K. Ganguly is supported by Senior Research Fellowship (SRF) from Council of Scientific & Industrial Research (CSIR), Human Resource Development Group, Government. of India. T. Saha and D. Sengupta are supported by Senior Research Fellowships (SRF) from University Grants Commission (UGC), Govt. of India.

Compliance with ethical standards

Conflict of interest

All the authors gave approval for submission of the current version of the manuscript for publication and have full access to the study data. Authors declare no conflict of interest with respect to this article.

Ethical approval and informed consent from patients

Not applicable for this study.

Supplementary material

403_2019_1891_MOESM1_ESM.pdf (373 kb)
Supplementary material 1 (PDF 373 KB)
403_2019_1891_MOESM2_ESM.pdf (264 kb)
Supplementary material 2 (PDF 263 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of GeneticsUniversity of CalcuttaKolkataIndia

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