Table 2.
Results of Previously Reported Loci
| Genotype p-value* | Combined | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome band | Proposed Candidate | SNPID+ | Risk allele (freq)^ | Stage 1 | Stage 2 | Stage 3 | Controls/ cases | Genotype p-value | OR het (95% CI) | OR hom (95% CI) |
| 10q26.13 | FGFR2 | rs2981579 | T (41%) | 4.36×10−5 | 1.22×10−6 | - | 5283, 5439 | 1.79×10−10 | 1.17 (1.07–1.27) | 1.46 (1.30–1.62) |
| 16q12.1 | TOX3 | rs3803662 | T (27%) | 5.3×10−2 | 6.82×10−9 | - | 5281, 5434 | 1.11×10−9 | 1.16 (1.07–1.27) | 1.55 (1.34–1.78) |
| 5q11.2 | MAP3K1 | rs16886165 | G (15%) | 3.1×10−2 | 1.17×10−5 | - | 5283, 5440 | 5.00×10−7 | 1.23 (1.12–1.35) | 1.65 (1.30–2.10) |
| 8q24.21 | rs1562430 | A (57%) | 1.44×10−2 | 4.74×10−4 | 5285, 5440 | 1.28×10−5 | 0.84 (0.77–0.92) | 0.79 (0.71–0.89) | ||
| 2q35 | rs13387042 | A (51%) | 1.10×10−2 | 1.48×10−6 | 5285, 5433 | 2.10×10−8 | 0.80 (0.73–0.87) | 0.74 (0.67–0.83) | ||
| 11p15.5 | LSP1 | rs3817198 | C (32%) | 5.36×10−1 | 1.16×10−1 | 4.34×10−1 | 10316, 9408 | 6.51×10−2 | 1.02 (0.96–1.08) | 1.12 (1.02–1.23) |
| 5p12 | rs4415084 | T (41%) | 1.5×10−3 | 1.6×10−2 | 1.6×10−2 | 10293, 9367 | 4.53×10−5 | 1.09 (1.03–1.17) | 1.20 (1.11–1.31) | |
| 5p12 | rs10941679 | G (26%) | - | - | 5.5×10−3 | 5490, 4575 | 1.12 (1.03–1.22) | 1.20 (1.03–1.41) | ||
*
Adjusted genotype test with 2 df
+
SNPID corresponds to dbSNP ID (http://www.ncbi.nlm.nih.gov/projects/SNP/)
^
Estimated from controls in the combined (Stages 1–3) analysis
The results of the genotype and trend tests, both adjusted and unadjusted are presented in Supplemental Table 1.