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 located in the non-coding 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.