In this study, we applied the RHM method to primary biliary cholangitis (PBC) in 5643 Japanese individuals, and identified three new loci at the genome-wide significance level (STAT4, ULK4, and KCNH5), two of which (ULK4 and KCNH5) have not been found associated with PBC in any population previously. The gene discussed is STAT4; the disease is primary biliary cholangitis.