It is not yet known if and how common IBD-associated SNPs affect the expression of PTPN2. We observed that the lead IBD SNP at 18p11.21 (rs80262450; 18-12818923-G-A) is associated with higher risk of IBD and with increased usage of splice junction chr18:12,817,365-12,818,944 (Fig. 6b, d and Supplementary Fig. 22). The gene discussed is PTPN2; the disease is inflammatory bowel disease.