Table 2. Associations Between SNPs and Stage IV vs. Stage I/II Colon Cancers for Top 20 SNPs Selected from Discovery Dataset for Replication.
| Discovery Dataset1 | Validation Dataset #11 | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Chr | BP | Nearest Gene | A1 | MAF2 | OR | 95% CI | P-value | A1 | MAF2 | OR | 95% CI | P-value |
| rs2024846 | 6 | 85575780 | TBX18 | LOC100289423 | A | 0.20 | 2.62 | (1.76, 3.92) | 1.20E-06 | A | 0.27 | 0.90 | (0.62, 1.30) | 2.15E-01 |
| rs72737810 | 4 | 149743890 | NR3C2 | LOC100287246 3 | G | 0.14 | 2.83 | (1.81, 4.44) | 2.73E-06 | G | 0.16 | 1.89 | (1.27, 2.82) | 9.12E-04 |
| rs60745952 | 4 | 149748994 | NR3C2 | LOC100287246 | G | 0.14 | 2.83 | (1.81, 4.44) | 2.73E-06 | C | 0.17 | 1.89 | (1.27, 2.80) | 8.05E-04 |
| rs73351705 | 8 | 114783818 | CSMD3 | TRPS1 | A | 0.03 | 5.53 | (2.54, 12.05) | 8.49E-06 | A | 0.05 | 1.25 | (0.61, 2.57) | 2.71E-01 |
| rs77801238 | 8 | 114825951 | CSMD3 | TRPS1 | G | 0.01 | 8.87 | (3.27, 24.11) | 9.35E-06 | C | 0.04 | 1.67 | (0.79, 3.51) | 8.97E-02 |
| rs74602504 | 8 | 114823103 | CSMD3 | TRPS1 3 | G | 0.01 | 8.87 | (3.27, 24.11) | 9.35E-06 | NA | NA | NA | NA | NA |
| rs76047883 | 4 | 149768284 | NR3C2 | LOC100287246 | A | 0.13 | 2.68 | (1.70, 4.23) | 1.18E-05 | NA | NA | NA | NA | NA |
| rs7737423 | 5 | 123132486 | CSNK1G3 | ZNF608 | A | 0.04 | 3.78 | (2.04, 7.00) | 1.26E-05 | NA | NA | NA | NA | NA |
| rs78793716 | 11 | 124941849 | SLC37A2 | A | 0.06 | 3.69 | (2.01, 6.77) | 1.30E-05 | A | 0.08 | 0.64 | (0.33, 1.27) | 3.98E-01 |
| rs13058496 | 22 | 17398812 | LOC440786 | G | 0.23 | 2.18 | (1.51, 3.13) | 1.38E-05 | G | 0.24 | 1.20 | (0.83, 1.73) | 1.72E-01 |
| rs6705378 | 2 | 240193889 | HDAC4 | G | 0.43 | 2.24 | (1.53, 3.26) | 1.44E-05 | G | 0.46 | 0.97 | (0.70, 1.34) | 7.70E-02 |
| rs11068687 | 12 | 118256497 | KSR2 | A | 0.18 | 2.35 | (1.58, 3.52) | 1.48E-05 | T | 0.20 | 1.04 | (0.70, 1.54) | 4.24E-01 |
| rs7669737 | 4 | 162361217 | FSTL5 | G | 0.38 | 2.16 | (1.50, 3.11) | 1.59E-05 | G | 0.42 | 1.21 | (0.87, 1.68) | 1.26E-01 |
| rs62377104 | 5 | 123074679 | CSNK1G3 | ZNF608 3 | C | 0.05 | 3.60 | (1.95, 6.63) | 2.00E-05 | G | 0.05 | 1.01 | (0.51, 2.00) | 4.87E-01 |
| rs1556055 | 10 | 17523142 | ST8SIA6 | PTPLA | G | 0.20 | 2.40 | (1.58, 3.64) | 2.08E-05 | G | 0.24 | 1.03 | (0.70, 1.50) | 4.47E-01 |
| rs16962543 | 19 | 29578972 | LOC148145 | UQCRFS1 | A | 0.06 | 3.34 | (1.87, 5.96) | 2.17E-05 | A | 0.10 | 0.60 | (0.31, 1.15) | 4.37E-01 |
| rs12367527 | 12 | 59398014 | LRIG3 | SLC16A7 | A | 0.09 | 2.62 | (1.65, 4.16) | 2.26E-05 | A | 0.13 | 0.83 | (0.50, 1.39) | 2.55E-01 |
| rs308420 | 4 | 123767943 | FGF2 | A | 0.04 | 4.33 | (2.14, 8.75) | 2.27E-05 | A | 0.06 | 0.97 | (0.49, 1.92) | 3.76E-02 |
| rs62451177 | 6 | 85559189 | TBX18 | LOC100289423 | G | 0.10 | 2.88 | (1.73, 4.80) | 2.29E-05 | NA | NA | NA | NA | NA |
| rs2203879 | 2 | 22186722 | LOC100129278 | KLHL29 | A | 0.02 | 6.47 | (2.63, 15.88) | 2.36E-05 | NA | NA | NA | NA | NA |
1 Adjusted for age, sex and first 2 principal components (PCs); analyses conducted using a log-additive genetic model in PLINK
2 MAF = Minor allele (A1) frequency in Stage I/II cases; 3 Redundant SNPs.