Haplotype Analysis Reveals Pleiotropic Disease Associations in the HLA Region Manuscript Supplementary Tables

Supplementary Table 1: Enrichment of GWAS hits in the HLA region for each trait group for all traits in FinnGen with at least one GWAS hit (MAF > 1%) anywhere in the genome. Supplementary Table 2: Manual trait group classification for the 269 non-redundant diseases with at least one significantly associated SNP (P < 1e-6; MAF > 1%) in the HLA region, by pathophysiology first (Category) and then by affected organ system (Subcategory). Supplementary Table 3: Haplotype and haplotype group statistics and assignments. Haplotype statistics are for all haplotypes with > 10 total copies for privacy policy reasons. Supplementary Table 4: Regression results for haplotype groups across all 3 blocks. The first tab has the data plotted in the heatmap of Figure 5, which is the values of the regression Z-scores rescaled to add back in the dropped haplotype group for each block. The next two tabs have the (non-rescaled) regression results for all traits, with and without jointly modeling with the relevant classical HLA alleles in the block. Supplementary Table 5: Regression results for the SNP-trait associations for significant SNP associations remaining after step-wise conditional analysis in the HLA region. Supplementary Table 6: Regression results for all allele associations for all traits, for both the approach jointly modeling alleles within a given block together (tab 1) and for the approach with one allele per regression (tab 2).