Table 1 Association results for SNVs identified in single variant association meta-analyses and taken forward to replication are provided

From: Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci

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

  1. 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)
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