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. Author manuscript; available in PMC: 2017 Dec 14.
Published in final edited form as: Nat Genet. 2017 Jan 9;49(2):262–268. doi: 10.1038/ng.3755

Figure 2. Association signal at the MHC is linked to the ancestral 8.1 haplotype.

Figure 2

(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.