We set parameters as described above and we used eQTLs in five tissue types from GTEx which are relevant to CD, i.e., Small Intestine, Colon Sigmoid, Colon Transverse, Stomach, and Whole Blood. Chromatin interaction mapping was performed using Hi-C data of two tissue types; Liver and Small Bowel from GSE87112. The MHC region and indels were excluded from the analysis. Since the input GWAS summary statistics only contained results from the discovery phase, we manually submitted the 71 reported lead SNPs to FUMA in addition to the independent lead SNPs that were identified as described above (Supplementary Data 7). Only protein-coding genes were used in mappings and enrichment of DEG in 53 tissue types, Canonical Pathways and GO terms were tested.
