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Primary biliary cholangitis (PBC) susceptibility loci have largely been discovered through single SNP association testing. In this study, we report genic haplotype patterns associated with PBC risk genome-wide in two Japanese cohorts. Among the 74 genic PBC risk haplotype candidates we detected with a novel methodological approach in a discovery cohort of 1,937 Japanese, nearly two-thirds were replicated (49 haplotypes, Bonferroni-corrected P < 6.8 × 10 −4 ) in an independent Japanese cohort (N = 949). Along with corroborating known PBC-associated loci ( TNFSF15 ,  HLA-DRA ), risk haplotypes may potentially model  cis -interactions that regulate gene expression. For example, one replicated haplotype association (9q32–9q33.1, OR = 1.7, P = 3.0 × 10 −21 ) consists of intergenic SNPs outside of the human leukocyte antigen (HLA) region that overlap regulatory histone mark peaks in liver and blood cells, and are significantly associated with  TNFSF8  expression in whole blood. We also replicated a novel haplotype association involving non-HLA SNPs mapped to  UMAD1  (7p21.3; OR = 15.2, P = 3.9 × 10 −9 ) that overlap enhancer peaks in liver and memory T h  cells. Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.

Genome-wide haplotype association analysis of primary biliary cholangitis risk in Japanese