From epistasis analysis, we found the most connected gene with other SNPs that synergistically conferred risks to Crohn's disease was MST1. In particular, MST1 rs144982232 showed interactions with other IBD genes, including JAK2, NOD2, ATG16L, VDR and STAT3, indicating a more complicated role of MST1 in Crohn's disease pathogenesis. Here, ATG16L1 is linked to inflammatory bowel disease.