Genes with a SNP with p<0.001 in immune-related processes that are significantly enriched in both GWAS.

Genes included are those that have a SNP with p<0.001 in the Harold GWAS, and are in the immune-related processes significantly enriched in both GWAS (Table 4). BCL3 is not included in the enrichment analysis (Tables 3 and 4) since it is in LD with APOE. Two genes, CLU and APOA4, are found in both cholesterol and immune-related GO processes. CR1 and CR2 are at the same locus, as are IL18RAP, IL18R1 and IL1RL1 (see Table 3). Although they do not share the same best SNP, they may be tagging the same signal. The same applies to HLA-DRB1, HLA-DRA, HLA-DOB, TAP2 and HLA-DQA1, which are all in the MHC region. The category-wide set-based analysis allows for such dependence between genes. Genes contributing to the enrichment signal from Harold et al. are in bold, genes contributing to the signal from Lambert et al. are in italic and genes contributing to the signal in both are in bold italic.