Functional analysis of the merged validated SNP list for PBC and PSC revealed significant over-representation of genes associated with immune responses (HLA-DQB1, HLA-DRB5, HLA-C, HLA-B, HLA-DPB1, HLA-DQA2, HLA-DQA1, and HLA-DRA; P = 0.023; Additional file 2: Table S3). This evidence concerns the gene HLA-DQA1 and primary biliary cholangitis.