Additional Supporting Information may be found in the online version of this article.

IBD_21912_sm_SuppFig1.tif2097KSupplementary Figure 1.
IBD_21912_sm_SuppTab1.doc68KSupporting Table 1: Phenotypes, genotypes and clinical details of adult patients and controls in study.
IBD_21912_sm_SuppTab2.doc34KSupporting Table 2: Phenotypes of early onset patients.
IBD_21912_sm_SuppTab3.doc4173KSupporting table 3: Differential methylation of CpG sites on genes.
IBD_21912_sm_SuppTab4.doc25KSupporting Table 4: Fold enrichments (and corresponding p values) for SNPs within 25kb, 100kb and 50kb (split into all, hyper methylated and hypo methylated SNPs) of known CD loci. Fold enrichment are the proportion of sites below various differential methylation FDR corrected significance cut offs over the proportion of all sites, table corresponds to data presented in Figure 1A and B.

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