We identified associations at the genome-wide significance level between three new loci (STAT4, ULK4, and KCNH5) and PBC in the Japanese population, two of which (ULK4 and KCNH5) have not been identified in any population previously; this result was obtained by applying RHM and could not be achieved with single-SNP GWAS only. Here, KCNH5 is linked to primary biliary cholangitis.