In the Discovery phase, six SNPs in four innate immunity genes (DEFA6, DEFB1, JAK3, and ACAA1) and 11 SNPs in nine NHL-related genes (INSL3, CHMP7, CASP7, RAD50, CHUK, TNFRSF8, CD79B, BCL2L11, and CLDN9) were significantly associated with gastric cancer risk (permutated p<0.01); and after the BH-FDR test for the genes in 42 sets of cases and controls, DEFA6 and DEFB1 in the innate immunity gene panel and INSL3 in the NHL-related gene panel were significantly associated with gastric cancer risk (BH-FDR p<0.1). This evidence concerns the gene CLDN9 and gastric cancer.