Table 3. Functional annotation of the variants that reached statistical significance for GxE with smoking status.
| Phenotype | rsID | BP | Locus | REF allele | EFF allele | Overlapped gene | Nearest upstream gene | Distance (BP) | Nearest downstream gene | Distance (BP) |
|---|---|---|---|---|---|---|---|---|---|---|
| Tumor size (cm) | Not yet assigned | 38247577 | 14q21.1 | CTGG | C | TTC6 (intronic) | – | – | – | – |
| rs35225990 | 46117489 | 13q14.13 | C | T | FAM194B (intronic) | – | – | – | – | |
| rs188958632 | 38266174 | 14q21.1 | G | A | TTC6 (intronic) | – | – | – | – | |
| rs180910528 | 79821806 | 6q14.1 | A | C | – | PHIP (protein coding) | 33853 | HMGN3 (protein coding) | 89,156 | |
| rs74603364 | 79509518 | 6q14.1 | C | T | – | RP3–390M24.1 (lincRNA) | 193765 | RP11–173D14.3 (lincRNA) | 9,914 | |
| rs187040828 | 79802426 | 6q14.1 | T | C | – | PHIP (protein coding) | 14473 | HMGN3 (protein coding) | 108,536 | |
| rs144383242 | 79489625 | 6q14.1 | G | T | – | RP3–390M24.1 (lincRNA) | 173872 | RP11–173D14.3 (lincRNA) | 29,807 | |
| rs117587674 | 79432536 | 6q14.1 | G | A | – | RP3–390M24.1 (lincRNA) | 116783 | RP11–173D14.3 (lincRNA) | 86,896 | |
| rs113705641 | 5375733 | 3p26.1 | A | G | – | AC026202.5 (lincRNA) | 77287 | AC027119.1 | 628,796 | |
| rs2937268 | 66553607 | 1p31.3 | C | T | PDE4B (intronic) | – | – | – | – |
GxE, gene-environment interaction; BP, base pair; rsID, SNP ID; SNP, single nucleotide polymorphism; REF, reference; EFF, effect.