provideddbSNP ID (Exome ID)Chr:PosEA/OAGeneConsequenceTraitDiscovery stageReplication stageNEAFDoEP-valueBeta (SE)P-valuers141611945 (exm118559)1:161771868G/AATF6MissenseCPD128,7460.0065%MAC = 9+2.95 × 10−70.184 (0.169)*P = 0.276 in African American samplesrs1190736 ** (exm1659559)X:136113464A/CGPR101MissenseCPD (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)6:111695887A/GREV3LMissenseSI346,68280.1%-4.52 × 10−8−0.023 (0.0034)9.7 x 10−12rs216195 (exm1276230)17:2203167G/TSMG6MissenseSI335,40627.3%-2.80 × 10−8−0.008 (0.0029)8.5 x 10-3rs11539157 (exm1643833)X:68381264A/CPJA1MissenseSI289,91716.5%+1.39 × 10−110.022 (0.0026)0.0158 (0.0033)0.0185 (0.0039)All samples: 5.40 x 10−17Males only: 1.30 x 10−6Females only: 2.20 x 10−6Non-Exome-chip SNVsrs126162192:104352495A/CTMEM182IntergenicSI112,81146.4%-5.49 × 10−8−0.015 (0.0027)5.5 x 10−8rs11506916:28168033G/AZSCAN9MissenseSI112,81134.8%-4.95 × 10−8−0.007 (0.0028)8.0 x 10-3rs28413349:128122320A/GGAPVD1IntronicSI112,81120.9%-2.28 × 10−8−0.009 (0.0033)7.5 x 10-3rs20266422:41813886C/TTOB2IntergenicSC51,04319.9%-1.02 × 10−8−0.011 (0.0050)2.1 x 10-2rs118953812:60053727A/GBCL11AIntergenicSI112,81134.2%-5.61 × 10−9−0.007 (0.0028)1.2 x 10-2rs1278011610:104821946A/GCNNM2IntronicSI112,81113.9%+9.19 × 10−100.017 (0.0039)1.1 x 10−5Novel 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
