In the present study we identified chromosome 3q13.33, which includes the genes ARHGAP31, TMEM39A, POGLUT1, TIMMDC1, and CD80, as a PBC susceptibility locus in the Japanese population by genome-wide meta-analysis based on whole-genome SNP imputation analysis of two distinct data sets of Japanese PBC-GWAS. This evidence concerns the gene POGLUT1 and primary biliary cholangitis.