Supplementary data 4. SNP functional annotation and a list of the pleiotropic SNPs identified between 18 AiDs

We identified that the AiD associated SNPs are enriched in the regulatory regions of the genome. Of those, 186 are pleiotropic SNPs (<i>i.e., </i>same loci associated with multiple AiDs) that were associated with more than two AiDs. Majority of them (N=60) are shared between Crohn's disease (CRD) and Ulcerative colitis (ULC). We have presented a list of pleiotropic SNPs and the associated diseases in Table 2. For disease abbreviations, check Supplementary data 1.