After correcting for multiple comparisons, only two SNPs, DEFA6 rs2738120 and DEFB1 rs2702829, remained marginally significant for gastric cancer (FDR = 0.08 and FDR = 0.08, respectively), which showed an increased risk for gastric cancer (OR [95% CI] = 4.1 [1.6–10.4] and 2.9 [1.3–6.1], respectively). Here, DEFA6 is linked to gastric cancer.