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. Author manuscript; available in PMC: 2020 Jun 1.
Published in final edited form as: Biol Psychiatry. 2018 Dec 6;85(11):946–955. doi: 10.1016/j.biopsych.2018.11.024

Table 1.

All nonsynonymous/loss of function variants with posterior probability of association > .80 from one of the two fine mapping methods.

SNP REF/ALT N ALT AF GWAS p−value Beta SE Direction Annotation Posterior Probability of Association Number SNPs (Low Frequency Coding SNPs) in 95% Credible Interval
W/out Functional Prior W/ Functional Prior (fgwas) W/out Functional Prior W/ Functional Prior (fgwas)
Cigarettes per Day (CigDay)
rs36015615a G/A 69,951 .0002 3.2×10−8 1.2 .210 ==+=++=+=X=X+X+++ Nonsynonymous [STARD3] .82 .62 8,997 (6211) 11302 (6232)
rs16969968 G/A 153,918 .34 2.5×10−139 .096 .0038 +−++−+++++−++++++ Nonsynonymous [CHRNA5] .84 .92 2(0) 2 (0)
Drinks per Week (DrnkWk)
rs1260326 T/C 357,854 .61 4.6×10−40 0.032 .0024 +++++++++−−++++++ Nonsynonymous [GCKR] 1.0 1.0 1 (0) 1 (0)
rs1229984 T/C 334,588 .98 2.3×10−173 0.25 .0088 =+−XXXX+XXXX=++++ Nonsynonymous [ADH1B] 1.0 1.0 1 (1) 1 (1)
rs28929474 C/T 357,854 .02 2.2×10−11 −0.057 .0085 −−++−−−−−+++−−−−+ Nonsynonymous [SERPINA1] .95 1.0 1 (1) 1 (1)
rs1800566 G/A 357,854 .18 2.00×10−8 0.017 .0031 +++++++++++−−+++− Nonsynonymous [NQO1] .32 .97 103 (0) 1 (0)
Smoking Initiation (SmkInit)
rs2232423 A/G 433,216 .11 1.40×10−8 −0.019 .0034 −+−+−−−+−−−−−− Nonsynonymous [ZSCAN12] .84 .64 502 (0) 2 (0)
rs35891966 G/A 433,216 .07 1.30×10−8 −0.024 .0042 −−−+−+−−−++−−− Nonsynonymous [NAV2] .98 1.0 1 (0) 1 (0)
rs147052174 G/T 433,216 .02 1.2×10−7 .043 .0080 +++++++++−++++ Nonsynonymous [FAM163A] .81 1.0 2432(66) 1 (0)
rs6265 C/T 433,216 .19 1.9×10−10 −.017 .0030 ++−++−++−−+−−− Nonsynonymous [BDNF] .32 .83 25(0) 2 (0)
rs61754158 C/T 433,216 .01 1.4×10−6 −.055 .0114 −−+−+−−−=+=−+− Nonsynonymous [HEATR5A] .39 .87 9742(195) 9742 (195)
rs34967813 A/G 433,216 .31 8.1×10−7 −.011 .0023 −−−−+−−+−−+−−− Nonsynonymous [RYR2] .14 .98 7413(56) 1 (0)
a

rs36015615 did not replicate in two additional datasets. See results section.

Note: REF=reference allele on GRCh37, ALT=alternate allele, N=sample size across all studies that genotyped the variant, ALT AF=allele frequency of the alternate allele estimated in the meta−analysis. A variant is considered “rare” if MAF < .01, and low frequency if .01 ≤ MAF < .05. In the DIRECTION column each symbol represents the contribution of one of the studies. A “+” indicates the ALT allele had a positive effect in that study; “−” indicates a negative effect. A “=“ indicates the variant was monomorphic and “X” indicates it was absent in that study. The order of studies for CigDay and DrnkWk was ARIC, UKB, COGA, FINNTWIN, FUSION, GECCO, HRS, ID1000, MEC, METSIM, MHI, MCTFR, NAGOZALC, NESCOG, SardiNIA, TwinsUK, and WHI. For SmkInit the order is the same except COGA and MCTFR were not available. See the supplemental materials for study acronym explanations.