Table 2. Significant SNPs for candidate genes involved in downstream signaling pathways activated by CagA associated with gastric cancer in the discovery phase.
GENE | db SNP ID | #SNPsa | MAF (%)b | CHRc | CHRposition | Raw p-value d * | Permutated p-value e | OR (95% CI)f |
ERK | rs5999749g | 13 | C ( 9.4) | 22 | 20517660 | 0.0012 | 0.0011 | 2.83 (1.42–5.65) |
Dock180 | rs9418677g , h | 103 | C (40.5) | 10 | 128695397 | 0.0052 | 0.0048 | 1.90 (1.18–3.05) |
rs4635002g | A (11.3) | 128752669 | 0.0119 | 0.0168 | 0.44 (0.18–1.07) | |||
rs7068941 | A (11.8) | 128718078 | 0.0418 | 0.0667 | 0.41 (0.17–0.99) | |||
rs7917277 | T (11.8) | 128754664 | 0.0418 | 0.0667 | 0.41 (0.17–0.99) | |||
rs9418832 | A (11.8) | 128757891 | 0.0418 | 0.0667 | 0.41 (0.17–0.99) | |||
rs9418737 | A (11.8) | 128757840 | 0.0418 | 0.0667 | 0.41 (0.17–0.99) | |||
C3G | rs10901081g | 30 | A (21.2) | 9 | 133586496 | 0.0109 | 0.0103 | 0.49 (0.27–0.91) |
rs7853122g | G (17.1) | 133570432 | 0.0199 | 0.0248 | 0.47 (0.24–0.94) | |||
rs4991743 | A (17.1) | 133597568 | 0.0199 | 0.0248 | 0.47 (0.24–0.94) | |||
rs7047157 | C (17.1) | 133503399 | 0.0199 | 0.0248 | 0.47 (0.24–0.94) | |||
rs4474069 | T (17.5) | 133501207 | 0.0248 | 0.0260 | 0.49 (0.25–0.98) | |||
rs1544305 | C (16.5) | 133480201 | 0.0355 | 0.0361 | 0.50 (0.25–1.02) | |||
Rap1 | rs530801g | 16 | A (34.5) | 1 | 111968778 | 0.0184 | 0.0186 | 0.57 (0.35–0.94) |
rs558989 | G (32.9) | 112043318 | 0.0207 | 0.0209 | 0.57 (0.34–0.95) | |||
rs17028287 | T ( 4.2) | 112046321 | 0.0215 | 0.0238 | 2.46 (0.96–6.28) | |||
rs571020 | G (33.9) | 112002851 | 0.0244 | 0.0266 | 0.59 (0.37–0.96) | |||
rs846261 | A (32.4) | 112054920 | 0.0305 | 0.0378 | 0.60 (0.36–0.99) | |||
Src | rs747182g | 5 | G (12.9) | 20 | 35416303 | 0.0224 | 0.0188 | 1.80 (0.99–3.26) |
CrkL | rs5761368 | 2 | A ( 9.4) | 22 | 19607471 | 0.0281 | 0.0344 | 2.00 (1.01–3.96) |
Mek | rs4255740 | 6 | T (35.3) | 15 | 64559061 | 0.0432 | 0.0426 | 0.58 (0.35–0.98) |
rs16949924 | C (35.3) | 64514651 | 0.0432 | 0.0426 | 0.58 (0.35–0.98) | |||
Crk | rs8064892 | 6 | C (14.7) | 17 | 1283132 | 0.0477 | 0.0602 | 0.51 (0.24–1.07) |
rs8073032 | C (14.7) | 1283157 | 0.0477 | 0.0602 | 0.51 (0.24–1.07) |
Total number of selected SNPs within each candidate gene.
Minor allele frequency among controls.
Chromosome number.
Raw p-values calculated in the trend model with a cut-off level ≤0.01.
100,000 permutations for single SNP in the trend model.
Adjusted for age, smoking (never vs. ever), H. pylori infection (positive vs. negative) and CagA seropositivity (positive vs. negative).
Seven representative SNPs with a raw or permutated p value<0.02 identified in the discovery phase were analyzed in the extension phase.
Excluded due to a SNP call rate <95%.
*All BH-FDR p-values were not significant (p>0.05).