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. Author manuscript; available in PMC: 2019 Jul 14.
Published in final edited form as: Nat Genet. 2019 Jan 14;51(2):237–244. doi: 10.1038/s41588-018-0307-5

Table 1. Nonsynonymous sentinel variants.

The sentinel variant in approximately 4% of loci was nonsynonymous. Shown here are all nonsynonymous sentinel variants, and all nonsynonymous variants in near-perfect LD with a sentinel variant. If the listed gene was also associated (through single variant or gene-based test) with another phenotype, that phenotype is listed in parentheses. Several genes have been implicated in previous studies of substance use/addiction, including CHRNA5, BDNF, GCKR, and ADH1B.

Phenotype Gene rsID Chr Position REF ALT AF Beta p N Q
CigDay (SmkCes) CHRNA5 rs16969968a 15 78,882,925 G A .34 .075 1.2×10−278 330,721 .34
CigDay HIST1H2BE rs7766641 6 26,184,102 G A .27 −.014 2.9×10−10 335,553 .78
CigDay (AgeSmk) GRK4 rs1024323 4 3,006,043 C T .38 −.012 8.7×10−9 337,334 .17
SmkInit REV3L rs462779a 6 111,695,887 G A .81 −.019 4.5×10−29 1,232,091 .67
SmkInit (DrnkWk) BDNF rs6265 11 27,679,916 C T .20 −.016 2.8×10−19 1,232,091 .13
SmkInit RHOT2 rs1139897 16 720,986 G A .23 −.012 1.8×10−15 1,232,091 .61
SmkInit (DrnkWk) ZNF789 rs6962772a 7 99,081,730 A G .15 −.015 2.1×10−14 1,232,091 .92
SmkInit BRWD1 rs4818005a 21 40,574,305 A G .58 −.010 3.9×10−14 1,232,091 .75
SmkInit ENTPD6 rs6050446 20 25,195,509 A G .97 .035 8.8×10−13 1,225,969 .33
SmkInit RPS6KA4 rs17857342a 11 64,138,905 T G .38 −.010 9.8×10−12 1,232,091 .16
SmkInit FAM163A rs147052174 1 179,783,167 G T .02 .037 2.3×10−10 1,232,091 .59
SmkInit PRRC2B rs34553878 9 134,907,263 A G .11 .016 1.2×10−9 1,232,091 .28
SmkInit ADAM15 rs45444697a 1 155033918 C T .21 .010 5.3×10−9 1,232,091 .46
SmkInit MMS22L rs9481410a 6 97,677,118 G A .76 .010 1.1×10−8 1,232,091 .04
SmkInit QSER1 rs62618693 11 32,956,492 C T .04 −.020 2.1×10−8 1,232,091 1.00
DrnkWk ADH1B rs1229984 4 100,239,319 T C .96 .060 2.2×10−308 941,280 .05
DrnkWk GCKR rs1260326 2 27,730,940 T C .60 .008 8.1×10−45 941,280 .10
DrnkWk SLC39A8 rs13107325 4 103,188,709 C T .07 −.009 1.5×10−22 941,280 .33
DrnkWk SERPINA1 rs28929474 14 94,844,947 C T .02 −.012 1.3×10−11 941,280 .50
DrnkWk (SmkInit) ACTR1B rs11692465 2 98,275,354 G A .09 .008 2.5×10−11 937,516 .40
DrnkWk TNFSF12–13 rs3803800 17 7,462,969 A G .79 .004 1.5×10−10 941,280 .67
DrnkWk HGFAC rs3748034 4 3,446,091 G T .14 −.005 1.7×10−8 941,280 .65

Note: Phenotype abbreviations are defined in Figure 1. Chr=Chromosome; REF=reference allele; ALT=alternate allele; AF=allele frequency of ALT allele; Q=Cochrane’s Q statistic p-value.

a

These variants were not themselves sentinel, but were in near-perfect LD with a sentinel variant (R2 >.99, from the 1000 Genomes European population). The scale of Beta is on the unit of the standard deviation of the phenotype. For binary phenotypes the standard deviation was calculated from the weighted average prevalence across all studies included in the meta-analysis (available in Supplementary Table 7).