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. Here, KCNH5 is linked to biliary liver cirrhosis.