Integration of GWAS with the eQTLs and mQTLs of these DEGs from the peripheral blood prioritized five putative OS genes and their regulatory elements associated with CD onset: BAD, SHC1, STAT3, MUC1, and GPX3. Moreover, the integration of intestinal eQTL data also identified five candidate causal genes, of which MUC1, CD40, and PRKAB1 were involved in intestinal gene–microbiota interactions through further colocalization analysis. This evidence concerns the gene CD40 and Cowden disease.