EvoSNP-DB: A database of genetic diversity in East Asian populations

Abstract

Genome-wide association studies (GWAS) have becomepopular as an approach for the identification of large numbersof phenotype-associated variants. However, differences ingenetic architecture and environmental factors mean that theeffect of variants can vary across populations. Understandingpopulation genetic diversity is valuable for the investigation ofpossible population specific and independent effects ofvariants. EvoSNP-DB aims to provide information regardinggenetic diversity among East Asian populations, includingChinese, Japanese, and Korean. Non-redundant SNPs (1.6million) were genotyped in 54 Korean trios (162 samples) andwere compared with 4 million SNPs from HapMap phase IIpopulations. EvoSNP-DB provides two user interfaces for dataquery and visualization, and integrates scores of geneticdiversity (Fst and VarLD) at the level of SNPs, genes, andchromosome regions. EvoSNP-DB is a web-based applicationthat allows users to navigate and visualize measurements ofpopulation genetic differences in an interactive manner, and isavailable online at [http://biomi.cdc.go.kr/EvoSNP/]. [BMBReports 2013; 46(8): 416-421]

Keywords

• Database
• Genetic diversity
• GWAS
• Population genetics
• SNP