(a) The residual MHC association after conditioning on the lead SNP (rs9279411). (b) Allelic associations at class I and II HLA genes. For each allele, odds ratios (OR), 95% confidence intervals, and P values are shown. The significance threshold was corrected for the number of independent tests (P < 2.5 x 10-4). Alleles that are components of the ancestral MHC AH8.1 haplotype are shaded blue (full AH8.1 annotation: HLA A*01:01, C*07:01, B*08:01, DRB1*03:01, DRB3*01:01, DQA1*05:01, DQB1*02:01). HLA DRB1*0103 (the strongest IBD susceptibility allele, ref 28) is included for comparison (shaded grey). (c) The residual MHC association after cross-conditioning on the lead HLA allele (HLA-B*08:01). In panels a and c the -log10(P) of SNPs are plotted against chromosomal position. Only selected genes from class I and II regions are shown for clarity.