Type 2 diabetes mellitus (T2D) is a multi-factorial polygenic disease. To date, T2D GWAS loci (~75) are insufficient to dissect the complex genetic structure underlying etiological heterogeneity. Epistasis has long been suggested to be important to understanding of the missing heritability problem. To identify epistatic effects on T2D, we conducted a multi-association analysis as complementary to the current single SNP-based GWAS. A total of 8,842 samples from the Korea Association Resource (KARE) project were analyzed for multi-traits (HbA1c, fasting plasma glucose and plasma glucose 2-hour after ingestion of 75 g oral glucose). Our study not only confirmed previously reported T2D loci but also identified a novel gene. These results could provide additional insight into the genetic regulation of T2D but require further replicative efforts to confirm the findings.