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Table 2 Top 50 candidate SNPs possibly associated with nicotine dependence (TDS score)

From: Associations between the orexin (hypocretin) receptor 2 gene polymorphism Val308Ile and nicotine dependence in genome-wide and subsequent association studies

Rank CHR SNP Position Genotypeb(TDS ≥ 3) Genotypeb(TDS < 3) χ2 p Related gene Region MAF TFBS Splicing Polyphen
1 18 rs11662608 60876992 7/38/33 22/36/11 18.28 1.90E-05 CDH7 5′ flanking 0.44897959 - - -
2 2 rs10490099 58991504 6/40/33 0/19/50 16.33 5.33E-05 LOC730134 3′ flanking 0.23986486 - - -
3 13 rs17056451 37163539 8/44/24 2/22/45 16.24 5.59E-05 TRPC4 intron 0.29655172 - - -
4 4 rs13112895 60509294 18/40/21 5/24/40 16.17 5.80E-05 LOC644419 5′ flanking 0.37162162 - - -
5 9 rs10973120 36885382 5/20/54 9/38/22 15.88 6.76E-05 PAX5 intron 0.29054054 - - -
6 18 rs611411 60899889 26/43/10 10/31/28 15.82 6.95E-05 CDH7 5′ flanking 0.49324324 - - -
7 18 rs176136 60936692 18/43/18 5/28/36 15.61 7.80E-05 CDH7 5′ flanking 0.39527027 - - -
8 18 rs176121 60958616 14/42/23 4/23/42 15.28 9.28E-05 CDH7 5′ flanking 0.34121622 - - -
9 2 rs985162 129883821 10/44/25 0/29/40 15.18 9.76E-05 LOC402102 5′ flanking 0.31418919 - - -
10 5 rs1366589 84922599 11/35/33 4/12/53 15.17 9.81E-05 LOC645181 3′ flanking 0.26013514 - - -
11 18 rs12962611 18303667 5/47/27 0/25/44 15.1 1.02E-04 CTAGE1 5′ flanking 0.27702703 - - -
12 1 rs909530 169349798 16/46/17 4/31/34 15.06 1.04E-04 FMO3 syna 0.39527027 - + -
13 1 rs12032382 207272695 0/10/69 0/28/41 15.05 1.05E-04 LOC391157 5′ flanking 0.12837838 - - -
14 13 rs9532107 37187961 2/24/53 13/28/28 15.01 1.07E-04 TRPC4 intron 0.27702703 - - -
15 5 rs7719216 8023898 3/20/56 7/36/26 14.97 1.09E-04 MTRR 3′ flanking 0.25675676 - - -
16 4 rs923665 38214103 0/5/72 1/20/46 14.96 1.10E-04 NULL 3′ flanking 0.09375 - - -
17 15 rs28716882 21552860 3/28/48 0/8/61 14.94 1.11E-04 NDN 5′ flanking 0.14189189 - - -
18 2 rs875063 111529556 10/32/37 20/37/12 14.92 1.12E-04 ACOXL intron 0.43581081 - - -
19 4 rs13144500 183475934 1/9/69 3/26/40 14.91 1.13E-04 ODZ3 intron 0.14527027 - - -
20 6 rs1772253 24528213 4/35/40 0/14/55 14.76 1.22E-04 MRS2L intron 0.19256757 - - -
21 4 rs2866688 78968066 4/38/37 2/11/55 14.74 1.24E-04 CNOT6L 5′ flanking 0.20748299 - - -
22 12 rs17120420 56856068 18/44/16 4/34/31 14.45 1.44E-04 LOC338805 5′ flanking 0.41496599 - - -
23 17 rs16946572 12604902 7/30/42 17/35/17 14.32 1.54E-04 MYOCD intron 0.38175676 - - -
24 18 rs4328535 70129056 12/39/28 0/28/41 14.16 1.68E-04 DKFZP781G0119 5′ flanking 0.30743243 + - -
25 16 rs10514585 81841839 7/43/29 22/35/12 14.16 1.68E-04 CDH13 intron 0.45945946 - - -
26 16 rs1379652 17304099 13/39/25 2/26/41 14.09 1.74E-04 XYLT1 intron 0.32534247 - - -
27 6 rs2496167 13450101 9/33/37 17/40/12 13.91 1.92E-04 TBC1D7 5′ flanking 0.4222973 - - -
28 11 rs623312 31864040 19/43/17 5/32/32 13.76 2.08E-04 LOC729605 5′ flanking 0.41554054 - - -
29 2 rs1403858 36566018 0/23/55 0/4/65 13.7 2.14E-04 CRIM1 intron 0.09183673 - - -
30 6 rs1591996 8291461 0/3/76 0/17/52 13.69 2.16E-04 SLC35B3 3′ flanking 0.06756757 - - -
31 9 rs4877369 89514689 8/26/45 19/30/20 13.65 2.20E-04 DAPK1 3′ flanking 0.37162162 - - -
32 16 rs17765854 64608419 21/43/15 7/31/31 13.63 2.22E-04 CDH5 5′ flanking 0.43918919 - - -
33 5 rs540375 152858920 2/23/54 0/5/64 13.59 2.27E-04 GRIA1 intron 0.10810811 - - -
34 16 rs2305689 69354016 10/30/39 19/36/14 13.48 2.41E-04 VAC14 intron 0.41891892 - - -
35 8 rs2975701 10147867 0/8/71 1/23/45 13.44 2.47E-04 MSRA intron 0.11148649 - - -
36 2 rs1567852 174440084 1/22/56 0/4/65 13.33 2.61E-04 LOC344178 3′ flanking 0.09459459 - - -
37 7 rs1540893 143398486 18/31/29 2/26/41 13.27 2.70E-04 OR2A25 5′ flanking 0.32993197 + - -
38 1 rs6686733 4663049 4/28/47 0/10/59 13.26 2.71E-04 AJAP1 intron 0.15540541 - - -
39 13 rs9555699 109898019 3/28/48 12/33/24 13.12 2.92E-04 COL4A2 intron 0.30743243 - - -
40 15 rs10851750 63908644 6/26/47 17/29/23 13.03 3.06E-04 DENND4A 5′ flanking 0.34121622 - - -
41 10 rs520887 78720167 3/29/47 0/10/59 12.98 3.15E-04 KCNMA1 intron 0.15202703 - - -
42 6 rs573668 13446548 1/30/48 11/32/26 12.94 3.21E-04 TBC1D7 5′ flanking 0.29054054 - - -
43 20 rs4810359 40624749 10/30/39 1/16/52 12.84 3.39E-04 PTPRT intron 0.22972973 - - -
44 12 rs10771391 27966867 23/41/15 6/36/27 12.84 3.40E-04 PTHLH 3′ flanking 0.45608108 - - -
45 14 rs2415449 37667678 13/41/25 2/28/39 12.83 3.42E-04 LOC729122 intron 0.33445946 - - -
46 7 rs3807171 37875304 11/39/29 2/23/44 12.82 3.43E-04 TXNDC3 intron 0.2972973 - - -
47 4 rs7667301 53395322 3/31/45 12/35/22 12.79 3.48E-04 RASL11B 5′ flanking 0.32432432 - - -
48 17 rs2188889 13178372 3/27/49 10/35/24 12.72 3.62E-04 HS3ST3A1 3′ flanking 0.2972973 - - -
49 5 rs6875661 54360379 9/37/33 16/43/10 12.65 3.76E-04 GZMK intron 0.43918919 - - -
50 7 rs2058024 25742215 15/39/25 3/27/39 12.57 3.92E-04 LOC646588 5′ flanking 0.34459459 - - -
  1. CHR, chromosome number; Position, chromosomal position (bp); Related gene, the nearest gene from the SNP site;
  2. a, coding region (synonymous polymorphism);
  3. b, distribution of genotype (homozygote of minor allele/heterozygote/homozygote of major allele);
  4. MAF, minor allele frequency; TFBS, SNPs located at a transcription factor-binding site (TFBS) of a gene;
  5. Splicing, SNPs located at exonic splicing enhancer (ESE) or exonic splicing silencer (ESS);
  6. Polyphen, predicted possible impact of an amino acid substitution in nonsynonymous SNPs on the structure and function of a human protein by PolyPhen tool (http://genetics.bwh.harvard.edu/pph/)