Here we performed a fine-mapping study of the TNFSF15 locus in three large disease samples of leprosy (9,619 cases and 12,896 controls of Chinese ethnicity), CD (1,576 cases and 3,013 controls of Korean ethnicity) and PBC (1,594 cases and 1,529 controls of Japanese ethnicity); through conditional and haplotype analyses, we clearly demonstrated that there are two independent associations at both rs6478108/rs6478109 and rs4979462 for risk of CD and leprosy, and a single association at rs4979462 for risk of PBC. The gene discussed is TNFSF15; the disease is primary biliary cholangitis.