Analysis using a total of 11 507 cases and 38 904 controls identified two novel loci on 12q24.11-12 (rs6490061, P = 3.20 × 10<sup>-8</sup> with an odds ratio [OR] of 0.905) and 20q11.21 (rs2376549, P = 8.11 × 10<sup>-10</sup> with an OR of 1.109). rs6490061 is located at intron 19 of the CUX2 gene, and its expression was suppressed by Helicobacter pylori infection. rs2376549 is included within the gene cluster of DEFB families that encode antibacterial peptides.