Table 1.
Association results for SNVs identified in single variant association meta-analyses and taken forward to replication are provided
| dbSNP ID (Exome ID) | Chr:Pos | EA/OA | Gene | Consequence | Trait | Discovery stage | Replication stage | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| N | EAF | DoE | P-value | Beta (SE) | P-value | ||||||
| rs141611945 (exm118559) | 1:161771868 | G/A | ATF6 | Missense | CPD | 128,746 |
0.0065% MAC = 9 |
+ | 2.95 × 10−7 | 0.184 (0.169) | *P = 0.276 in African American samples |
| rs1190736 ** (exm1659559) | X:136113464 | A/C | GPR101 | Missense | CPD (PY) | 99,037 (96,824) | 46.6% (47.0%) | - | 1.40 × 10−11 (4.98 x 10−9) |
−0.028 (0.0041) −0.027 (0.0049) −0.028 (0.0073) |
All samples: 8.20 x 10−12 (2.70 x 10−11) Males only: 1.90 x 10−8 (6.0 x 10−8) Females only: 1.10 x 10−4 (7.1 x 10−4) |
| rs462779 (exm572256) | 6:111695887 | A/G | REV3L | Missense | SI | 346,682 | 80.1% | - | 4.52 × 10−8 | −0.023 (0.0034) | 9.7 x 10−12 |
| rs216195 (exm1276230) | 17:2203167 | G/T | SMG6 | Missense | SI | 335,406 | 27.3% | - | 2.80 × 10−8 | −0.008 (0.0029) | 8.5 x 10-3 |
| rs11539157 (exm1643833) | X:68381264 | A/C | PJA1 | Missense | SI | 289,917 | 16.5% | + | 1.39 × 10−11 |
0.022 (0.0026) 0.0158 (0.0033) 0.0185 (0.0039) |
All samples: 5.40 x 10−17 Males only: 1.30 x 10−6 Females only: 2.20 x 10−6 |
| Non-Exome-chip SNVs | |||||||||||
| rs12616219 | 2:104352495 | A/C | TMEM182 | Intergenic | SI | 112,811 | 46.4% | - | 5.49 × 10−8 | −0.015 (0.0027) | 5.5 x 10−8 |
| rs1150691 | 6:28168033 | G/A | ZSCAN9 | Missense | SI | 112,811 | 34.8% | - | 4.95 × 10−8 | −0.007 (0.0028) | 8.0 x 10-3 |
| rs2841334 | 9:128122320 | A/G | GAPVD1 | Intronic | SI | 112,811 | 20.9% | - | 2.28 × 10−8 | −0.009 (0.0033) | 7.5 x 10-3 |
| rs202664 | 22:41813886 | C/T | TOB2 | Intergenic | SC | 51,043 | 19.9% | - | 1.02 × 10−8 | −0.011 (0.0050) | 2.1 x 10-2 |
| rs11895381 | 2:60053727 | A/G | BCL11A | Intergenic | SI | 112,811 | 34.2% | - | 5.61 × 10−9 | −0.007 (0.0028) | 1.2 x 10-2 |
| rs12780116 | 10:104821946 | A/G | CNNM2 | Intronic | SI | 112,811 | 13.9% | + | 9.19 × 10−10 | 0.017 (0.0039) | 1.1 x 10−5 |
Novel smoking trait associated SNVs that replicated with P < 0.005 and had consistent direction of effect in discovery and replication are highlighted in bold. The replication sample size for smoking initiation (SI), cigarettes per day (CPD), pack-years (PY), and smoking cessation (SC) were 275,596, 80,015, 78,897, and 123,851 respectively. Chromosome (Chr) and position (Pos) for hg19 build 37. EA effect allele, OA other allele, Gene closest gene, N number of individuals, EAF effect allele frequency in the pooled samples, MAC minor allele count, DoE direction of effect, SE standard error. All SNVs had heterogeneity P > 0.02 in the discovery stage. *Replication was sought in 1,437 individuals of African American-ancestry from the HRS and COGA studies; **The beta(se) for the association of rs1190736 with PY in the replication stage was −0.026 (0.0039)