Table III.
SNPs with P value <0.001 in two-sided subset search or random-effect meta-analysesa
| rs10811474 | rs3731239 | rs10511729 | rs12683422 | |
|---|---|---|---|---|
| Location | 3′ of IFNW1 | CDKN2A intronic | 3′ of ELAVL2 | LINGO2 intronic |
| Effect alleleb | G | C | G | T |
| Meta-analysis | ||||
| Random-effect P c | 0.005 | 0.19 | 0.16 | 0.64 |
| Two-side subset searchd | ||||
| Combined P | 0.008 | 5.21×10 −4 | 0.006 | 6.99×10 −4 |
| P for positive effect | 0.001 | 3.96×10 −4 | 1.00 | 0.11 |
| Subsets with positive association | BrC, RCC | ESCC, GC, BC | — | — |
| P for negative effect | 0.89 | 0.12 | 7.93×10 −4 | 5.93×10 −4 |
| Subsets with negative association | — | — | LC, BrC | RCC, BC |
| Association with individual cancerse, OR (P) | ||||
| ESCC | 1.05 (0.31) | 1.33 (7.50×10 −6) | 1.04 (0.41) | — |
| GC | 1.04 (0.37) | 1.20 (0.007) | 1.08 (0.13) | — |
| PanC | 1.01 (0.83) | 0.95 (0.21) | 1.02 (0.62) | 0.88 (0.33) |
| RCC | 1.18 (9.19×10 −4) | 1.02 (0.66) | 0.95 (0.33) | 0.64 (2.86×10 −4) |
| LC | 1.08 (0.03) | 1.04 (0.22) | 0.89 (0.001) | 4.13 (0.11) |
| BrC | 1.21 (0.001) | 0.90 (0.08) | 0.83 (0.004) | NA |
| BC | 0.99 (0.78) | 1.09 (0.03) | 0.99 (0.79) | 0.71 (0.009) |
| PrC | 0.99 (0.87) | 0.94 (0.29) | 1.01 (0.88) | NA |
NA, not applicable; OR, odds ratio.
aSNPs were ordered by the chromosome location. Significant P for meta-analysis (P < 0.05/39 = 0.0013) or for analysis in individual outcomes (P < 0.01) was marked in bold.
bThe minor allele in the cancer outcome with the most significant P value.
cRandom-effect meta-analysis was conducted using GLIMMIX, accounting for overlapping subjects.
dResults were from ASSET, a subset-based association analysis for combining SNP-based results, accounting for overlapping subjects.
eORs and P values per one effect allele, obtained by random-effect meta-analysis (for LC) or unconditional logistic regression (for other cancers) adjusting for cancer-specific covariates.