The homozygous variant genotype of TLR4 T>C (rs1554973) (ORunadj: 0.67, 95% CI: 0.46–0.98, p = 0.04) and both the homozygous and the heterozygous variant genotypes of IL23R G>A (rs11209026) (ORadj: 0.43, 95% CI: 0.28–0.67, p = 2*10−4) and PTPN22 1858 G>A (rs2476601) (ORadj: 0.62, 95% CI: 0.46–0.85, p = 3*10−3) were associated with reduced risk of IBD (Table S1 and S2). Here, PTPN22 is linked to inflammatory bowel disease.