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) |
a
Total number of selected SNPs within each candidate gene.
b
Minor allele frequency among controls.
c
Chromosome number.
d
Raw p-values calculated in the trend model with a cut-off level ≤0.01.
e
100,000 permutations for single SNP in the trend model.
f
Adjusted for age, smoking (never vs. ever), H. pylori infection (positive vs. negative) and CagA seropositivity (positive vs. negative).
g
Seven representative SNPs with a raw or permutated p value<0.02 identified in the discovery phase were analyzed in the extension phase.
h
Excluded due to a SNP call rate <95%.
*All BH-FDR p-values were not significant (p>0.05).