Three cases (ARPC2, CPTP for IBD, and the secondary eQTL in PAM for JIA) fit the expected pattern, but three others have the counter-intuitive relationship where the eQTL is observed in one disease but the established GWAS association is with the opposite disease (PRDX6 and ADAM1A for RA, the secondary eQTL in GBAP1 for CD). This evidence concerns the gene CPTP and juvenile idiopathic arthritis.