In the primary scan of the discovery set, of the 362 SNPs selected from CagA-related genes in the signal transduction pathway, 24 SNPs in eight genes, ERK, Dock180, C3G, Rap1, Src, CrkL, Mek and Crk, were significantly associated with gastric cancer risk in the single SNP analysis (p<0.05). Here, RAPGEF1 is linked to gastric cancer.