Table 4.
Top Ten SNPs
| Control-Only | Control + Affected | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| SNP | MAF | Chr. | Gene | SMAT (1-DF) | min-adj p | GEE (4-DF) | SMAT (1-DF) | min-adj p | GEE (4-DF) |
| rs1056104 | 0.082 | 2 | GEMIN6 | 5.75 × 10−6 | 1.6 × 10−3 | 4.04 × 10−4 | 5.74 × 10−6 | 1.69 × 10−3 | 4.08 × 10−4 |
| rs6847801 | 0.073 | 4 | N/A | 9.72 × 10−7 | 1.65 × 10−3 | 4.18 × 10−6 | 9.81 × 10−7 | 1.66 × 10−3 | 4.23 × 10−6 |
| rs6451476 | 0.095 | 5 | CDH18 | 9.45 × 10−6 | 2.95 × 10−3 | 4.48 × 10−4 | 9.43 × 10−6 | 2.94 × 10−3 | 4.48 × 10−4 |
| rs4242066 | 0.090 | 5 | CDH18 | 9.50 ×10−8 | 8.61 × 10−7 | 2.76 × 10−7 | 9.53 × 10−8 | 8.53 × 10−7 | 2.77 × 10−7 |
| rs1391429 | 0.098 | 5 | CDH18 | 9.43 × 10−7 | 2.59 × 10−4 | 1.97 × 10−5 | 9.44 × 10−7 | 2.57 × 10−4 | 1.98 × 10−5 |
| rs4461636 | 0.093 | 5 | CDH18 | 1.41 ×10−7 | 2.47 × 10−5 | 1.78 × 10−6 | 1.41 × 10−7 | 2.46 × 10−5 | 1.79 × 10−6 |
| rs4866159 | 0.101 | 5 | CDH18 | 1.11 × 10−6 | 5.1 × 10−4 | 2.76 × 10−5 | 1.11 × 10−6 | 5.12 × 10−4 | 2.77 × 10−5 |
| rs1277769 | 0.112 | 10 | CACNB2 | 6.79 ×10−6 | 7.70 × 10−4 | 2.57 × 10−4 | 6.82 × 10−6 | 7.66 × 10−4 | 2.58 × 10−4 |
| rs17152064 | 0.054 | 10 | LHPP | 7.53 × 10−6 | 3.16 × 10−3 | 6.41 × 10−5 | 7.36 × 10−6 | 3.14 × 10−3 | 6.32 × 10−5 |
| rs10902443 | 0.127 | 12 | N/A | 9.27 × 10−6 | 9.76 × 10−3 | 6.36 × 10−4 | 9.29 × 10−6 | 9.73 × 10−3 | 6.44 × 10−4 |
Top SNPs from the GWAS scan with a 1-DF scaled common effect test SMAT for control-only (left) and control + affected (right) on the four square-root-transformed smoking behavior outcomes. Adjusted p values from single outcome and unadjusted p values from the 4-DF GEE tests are also listed for comparison; joint outcome analysis p values reported using unstructured correlation matrix (, ; ).