Table 2.
Associations with p ≤ 0.0001 in Genome-wide Analyses for Smoking Initiation in the Discovery Sample
| Index SNPs with p Value < 0.0001 |
SNPs in LD with Index SNP |
Corresponding Genes |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | Index SNP | BP | P | OR | Minor Allele | N_ LD | NS | 01a | 05b | 001c | 0001d | LD with Index SNP & p < 0.0001 | Gene Symbol | Typee | N_ SNPs | Location of Index SNP |
| 2 | rs4608580 | 98319575 | 7.905e-5 | 0.817 | C | 4 | 0 | 0 | 1 | 3 | 0 | VWA3B | O | 1 | Intronic | |
| 2 | rs10865016 | 98447822 | 9.671e-6 | 1.356 | A | 1 | 0 | 0 | 0 | 1 | 0 | CNGA3 | IC | 11 | Intronic | |
| 2 | rs787151 | 144489568 | 2.745e-5 | 1.304 | A | 2 | 0 | 0 | 1 | 1 | 0 | |||||
| 2 | rs4423615 | 165263737 | 5.290e-5 | 0.815 | G | 1 | 0 | 0 | 1 | 0 | 0 | GRB14 | O | 18 | Intronic | |
| 3 | rs1599903 | 39930070 | 5.423e-5 | 1.238 | C | 5 | 0 | 0 | 2 | 3 | 0 | MYRIP | O | 60 | Intronic | |
| 3 | rs9824246 | 73185415 | 9.951e-5 | 1.778 | G | 0 | 0 | 0 | 0 | 0 | 0 | PPP4R2 | O | 7 | Intronic | |
| 3 | rs16860281 | 149478045 | 7.340e-6 | 0.672 | C | 1 | 0 | 0 | 0 | 1 | 0 | |||||
| 4 | rs7692181 | 64329760 | 7.625e-5 | 1.238 | T | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 6 | rs2395670 | 37190787 | 3.698e-5 | 1.257 | A | 1 | 0 | 0 | 0 | 1 | 0 | FGD2 | O | 12 | Intronic | |
| 6 | rs9321013 | 125372620 | 4.946e-5 | 1.205 | A | 1 | 0 | 0 | 1 | 0 | 0 | RNF217 | E | 1 | Intronic | |
| 7 | rs7805247 | 2883300 | 5.680e-5 | 0.763 | C | 1 | 0 | 0 | 1 | 0 | 0 | |||||
| 7 | rs6960379 | 63194667 | 6.579e-5 | 0.650 | C | 1 | 0 | 0 | 0 | 0 | 1 | rs611097 | ||||
| 7 | rs2237781 | 126269001 | 4.017e-5 | 1.608 | A | 1 | 0 | 0 | 0 | 1 | 0 | GRM8 | GR | 121 | Intronic | |
| 7 | rs4725563 | 139107440 | 2.798e-5 | 0.777 | C | 2 | 0 | 0 | 1 | 1 | 0 | TBXAS1 | E | 38 | Intronic | |
| 8 | rs4509385 | 10217606 | 8.009e-5 | 0.818 | A | 1 | 0 | 0 | 0 | 1 | 0 | MSRA | O | 144 | Intronic | |
| 8 | rs6997956 | 136553572 | 8.479e-6 | 1.257 | A | 1 | 0 | 0 | 0 | 1 | 0 | KHDRBS3 | O | 13 | Intronic | |
| 9 | rs10121807 | 82366438 | 9.379e-5 | 0.729 | G | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 9 | rs10115383 | 100450087 | 7.691e-5 | 1.256 | A | 1 | 0 | 0 | 0 | 1 | 0 | |||||
| 10 | rs10999845 | 72910367 | 5.807e-5 | 1.320 | G | 1 | 0 | 0 | 0 | 1 | 0 | CDH23 | T | 77 | Intronic | |
| 10 | rs3949478 | 97463204 | 3.203e-5 | 0.773 | A | 1 | 0 | 0 | 0 | 1 | 0 | ENTPD1 | O | 10 | Intronic | |
| 10 | rs1856801 | 112382152 | 3.787e-5 | 1.414 | T | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 10 | rs7082195 | 112417439 | 4.374e-5 | 1.345 | T | 2 | 0 | 1 | 0 | 1 | 0 | RBM20 | O | 1 | Intronic | |
| 10 | rs10794595 | 124871492 | 4.333e-6 | 0.786 | T | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 11 | rs17477949 | 12175779 | 3.733e-5 | 1.239 | T | 4 | 0 | 2 | 1 | 1 | 0 | MICAL2 | O | 91 | Intronic | |
| 11 | rs12797615 | 85944331 | 4.278e-5 | 1.255 | C | 1 | 0 | 0 | 0 | 1 | 0 | ME3 | E | 61 | Intronic | |
| 11 | rs737383 | 92304523 | 9.648e-5 | 0.818 | C | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 11 | rs4379857 | 132688814 | 9.737e-5 | 0.645 | A | 0 | 0 | 0 | 0 | 0 | 0 | OPCML | TM | 345 | Intronic | |
| 12 | rs7313149 | 13719554 | 6.733e-5 | 0.779 | C | 1 | 0 | 0 | 0 | 0 | 1 | rs2192972 | GRIN2B | IC | 147 | Intronic |
| 12 | rs4759802 | 129932057 | 7.443e-5 | 0.734 | A | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 13 | rs327127 | 28416900 | 2.283e-5 | 0.623 | C | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 13 | rs17295389 | 81213800 | 6.500e-5 | 0.738 | A | 3 | 0 | 0 | 1 | 2 | 0 | |||||
| 14 | rs8009082 | 50569094 | 5.011e-5 | 0.794 | A | 6 | 0 | 0 | 2 | 2 | 2 | rs8005389, rs11157796 | TRIM9 | O | 64 | Intronic |
| 14 | rs17252296 | 50650671 | 8.594e-5 | 0.796 | C | 2 | 0 | 0 | 1 | 1 | 0 | |||||
| 14 | rs8019291 | 92000917 | 8.087e-6 | 0.709 | T | 1 | 0 | 0 | 0 | 0 | 1 | rs7154288 | SLC24A4 | T | 49 | Intronic |
| 14 | rs999986 | 94873609 | 7.324e-5 | 0.804 | A | 0 | 0 | 0 | 0 | 0 | 0 | |||||
| 15 | rs4774925 | 55391694 | 9.852e-5 | 1.237 | T | 1 | 0 | 0 | 1 | 0 | 0 | |||||
| 16 | rs12920919 | 9845481 | 1.000e-4 | 0.809 | C | 9 | 4 | 0 | 5 | 0 | 0 | |||||
| 18 | rs17739703 | 28777286 | 6.690e-5 | 1.473 | C | 0 | 0 | 0 | 0 | 0 | 0 | C18orf34 | O | 17 | Intronic | |
| 20 | rs283277 | 52970231 | 1.582e-5 | 1.315 | A | 9 | 0 | 0 | 6 | 3 | 0 | |||||
| 21 | rs928302 | 42683153 | 1.230e-5 | 0.659 | T | 1 | 0 | 0 | 0 | 1 | 0 | TMPRSS3 | P | 16 | Coding | |
| 22 | rs16982400 | 16272098 | 4.057e-5 | 1.355 | C | 0 | 0 | 0 | 0 | 0 | 0 | |||||
N = 3497. A logistic-regression test was performed for smoking initiation (yes/no), with sex and age as covariates. Headings and abbreviations indicate the following information: Chr, chromosome; Index SNP, SNP with p value smaller than 0.0001; BP, base pair position of the index SNP; P, p value of the index SNP; OR, odds ratio; N_LD, number of SNPs in LD (≥ 0.50) with the index SNP within a physical distance of 250 kb; NS, number of clumped SNPs that are not significant (p > 0.05); N_SNPs, number of SNPs measured in this gene; Gene symbol, name of the gene if the SNP is located in a gene or close to a gene (<50 kb).
Gene symbol: VWA3B denotes von Willebrand factor A domain-containing 3B; CNGA3 denotes Cyclic nucleotide-gated cation channel alpha 3; GRB14 denotes Growth factor receptor-bound protein 14; MYRIP denotes Rab effector MyRIP (Myosin-VIIa- and Rab-interacting protein); PPP4R2 denotes Protein phosphatase 4, regulatory subunit 2; FGD2 denotes FYVE, RhoGEF and PH domain-containing protein 2; RNF217 denotes IBR domain-containing protein 1; GRM8 denotes Metabotropic glutamate receptor 8 precursor; TBXAS1 denotes Thromboxane-A synthase; MSRA denotes Peptide methionine sulfoxide reductase; CDH23 denotes Cadherin-23 precursor; ENTPD1 denotes Ectonucleoside triphosphate diphosphohydrolase 1; RBM20 denotes Novel protein (Fragment); MICAL2 denotes Protein MICAL-2; ME3 denotes NADP-dependent malic enzyme, mitochondrial precursor; OPCML denotes Opioid-binding protein/cell-adhesion molecule precursor; GRIN2B denotes Glutamate [NMDA] receptor subunit epsilon-2 precursor; TRIM9 denotes Tripartite motif-containing protein 9; SLC24A4 denotes Sodium/potassium/calcium exchanger 4 precursor; C18orf34 denotes Uncharacterized protein C18orf34; TMPRSS3 denotes Transmembrane protease, serine 3.
Number of clumped SNPs 0.01 < p < 0.05.
Number of clumped SNPs 0.001 < p < 0.05.
Number of clumped SNPs 0.0001 < p < 0.001.
Number of clumped SNPs p < 0.0001.
Abbreviations are as follows: O, other; IC, ion channel; E, enzyme; GR, G protein coupled receptor; T, transporter; TM, transmembrane receptor; P, peptidase.