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Table 1 Top 50 candidate SNPs possibly associated with nicotine dependence (FTND score). CHR, chromosome number; Position, chromosomal position (bp); Related gene, the nearest gene from the SNP site

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(FTND ≥ 4) Genotypeb(FTND < 4) χ2 p Related gene Region MAF TFBS Splicing Polyphen
1 6 rs12333016 107205884 0/21/42 0/4/80 20.82 5.04E-06 QRSL1 intron 0.08503401 - - -
2 2 rs11890985 116384532 2/30/31 0/15/70 19.21 1.17E-05 DPP10 3′ flanking 0.16554054 - - -
3 13 rs7984684 43517893 0/17/43 8/45/31 19.1 1.24E-05 LOC121838 3′ flanking 0.27083333 - - -
4 5 rs1009069 167806516 2/22/39 0/9/76 16.41 5.11E-05 WWC1 intron 0.11824324 - - -
5 5 rs4958493 151090416 0/18/45 0/4/81 16.28 5.45E-05 ATOX1 3′ flanking 0.07432432 - - -
6 6 rs7754752 54272356 0/7/56 2/33/50 16.12 5.96E-05 TINAG 5′ flanking 0.14864865 - - -
7 5 rs4976553 167800531 4/33/26 28/39/18 15.56 8.01E-05 WWC1 intron 0.45945946 - - -
8 13 rs7323018 43513039 3/25/35 16/47/22 15.46 8.42E-05 LOC121838 3′ flanking 0.37162162 - - -
9 13 rs4631996 98096579 0/3/60 1/25/59 15.06 1.04E-04 LOC643193 5′ flanking 0.10135135 - - -
10 2 rs10176321 235561801 7/30/26 27/44/14 15 1.08E-04 SH3BP4 intron 0.47972973 - - -
11 13 rs1768047 98126380 0/6/57 2/30/53 14.99 1.08E-04 SLC15A1 3′ flanking 0.13513514 - - -
12 4 rs2390944 127169897 0/4/59 1/27/57 14.94 1.11E-04 LOC645841 5′ flanking 0.11148649 - - -
13 13 rs9533755 43530210 1/20/42 11/42/32 14.54 1.37E-04 LOC121838 3′ flanking 0.29054054 - - -
14 2 rs2042831 235521853 5/36/22 26/46/13 14.53 1.38E-04 SH3BP4 5′ flanking 0.48648649 + - -
15 2 rs1542604 131309515 3/22/38 1/9/75 14.47 1.42E-04 LOC730032 5′ flanking 0.13175676 + - -
16 1 rs188158 26770729 9/33/21 4/26/55 14.44 1.45E-04 RPS6KA1 intron 0.28716216 - - -
17 13 rs696938 92529022 8/26/29 3/17/65 14.37 1.50E-04 GPC6 5′ flanking 0.21959459 - - -
18 10 rs7924276 132704843 26/27/10 12/44/29 14.33 1.53E-04 TCERG1L 3′ flanking 0.49662162 - - -
19 12 rs6488995 124375941 13/32/18 5/32/48 14.24 1.61E-04 TMEM132B 5′ flanking 0.33783784 + - -
20 13 rs4772116 98100046 0/0/63 0/17/68 14.24 1.61E-04 LOC643193 5′ flanking 0.05743243 - - -
21 1 rs3895368 228949696 1/13/49 4/42/39 14.13 1.70E-04 CAPN9 5′ flanking 0.21959459 + - -
22 5 rs2973808 177699186 8/25/30 2/19/64 13.74 2.10E-04 COL23A1 intron 0.21621622 - - -
23 2 rs4668703 11052055 22/31/10 13/37/35 13.63 2.23E-04 KCNF1 3′ flanking 0.46621622 - - -
24 15 rs12591960 87909455 3/19/41 11/45/28 13.62 2.24E-04 C15orf42 5′ flanking 0.31292517 - - -
25 5 rs9314227 97581046 6/31/26 27/41/17 13.46 2.44E-04 LOC642909 5′ flanking 0.46621622 - - -
26 8 rs3862072 65564638 7/28/28 26/42/17 13.41 2.50E-04 BHLHB5 5′ flanking 0.45945946 - - -
27 15 rs4887435 84682665 7/26/30 0/24/61 13.23 2.76E-04 LOC727915 5′ flanking 0.21621622 - - -
28 8 rs7819541 22098096 0/4/59 4/22/59 13.12 2.92E-04 BMP1 intron 0.11486486 - - -
29 6 rs2021678 102140234 0/5/58 3/25/57 13.12 2.93E-04 GRIK2 intron 0.12162162 - - -
30 18 rs9303903 2433818 16/38/9 12/35/38 12.83 3.41E-04 METTL4 3′ flanking 0.43581081 - - -
31 6 rs16882180 52164345 11/35/17 6/31/48 12.83 3.42E-04 IL17A 3′ flanking 0.33783784 - - -
32 7 rs11771393 154410032 1/4/58 3/27/54 12.79 3.49E-04 PAXIP1 intron 0.13265306 - - -
33 6 rs17082273 152529619 0/2/61 0/21/64 12.78 3.50E-04 SYNE1 intron 0.0777027 - + -
34 16 rs11862729 14053599 6/38/19 3/31/51 12.77 3.53E-04 MKL2 5′ flanking 0.29391892 - - -
35 3 rs6807108 146970672 6/30/27 3/20/62 12.73 3.60E-04 LOC389156 3′ flanking 0.22972973 - - -
36 10 rs1909669 123376244 18/34/11 9/42/34 12.6 3.87E-04 LOC729426 intron 0.43918919 - - -
37 13 rs1927382 101940250 1/17/45 0/6/79 12.55 3.97E-04 FGF14 5′ flanking 0.08445946 - - -
38 2 rs17028222 60529867 1/10/52 3/37/45 12.52 4.03E-04 BCL11A 3′ flanking 0.18581081 - - -
39 6 rs2237204 16532935 14/31/18 6/33/46 12.51 4.04E-04 ATXN1 intron 0.35135135 - - -
40 21 rs2242936 39345341 0/8/55 1/32/52 12.44 4.20E-04 LOC391282 5′ flanking 0.14189189 - - -
41 7 rs715205 122188782 0/14/49 0/3/82 12.44 4.21E-04 CADPS2 intron 0.05743243 - - -
42 16 rs289741 55574975 7/27/29 19/51/15 12.4 4.29E-04 CETP intron 0.43918919 - - -
43 10 rs12416632 37323355 8/24/31 21/47/17 12.2 4.78E-04 LOC646348 5′ flanking 0.43581081 + - -
44 1 rs7512726 204899584 9/34/20 3/33/49 12.19 4.81E-04 DYRK3 3′ flanking 0.30743243 - - -
45 14 rs11627505 85145744 0/15/48 9/32/44 12.06 5.16E-04 FLRT2 5′ flanking 0.21959459 - - -
46 1 rs1891243 222754068 2/28/33 1/16/68 12.01 5.29E-04 WDR26 5′ flanking 0.16891892 - - -
47 17 rs2309381 5209436 24/29/10 11/48/26 11.99 5.35E-04 RABEP1 intron 0.49662162 - - -
48 2 rs10166654 236276002 9/25/29 26/42/17 11.97 5.41E-04 CENTG2 intron 0.46283784 - - -
49 7 rs10230426 18699683 2/27/34 1/15/69 11.89 5.66E-04 HDAC9 intron 0.16216216 - - -
50 6 rs2653349 55250296 0/15/48 0/4/81 11.8 5.92E-04 HCRTR2 non-syna 0.06418919 - + benign
  1. a, coding region (nonsynonymous polymorphism);
  2. b, distribution of genotype (homozygote of minor allele/heterozygote/homozygote of major allele);
  3. MAF, minor allele frequency; TFBS, SNPs located at a transcription factor-binding site (TFBS) of a gene;
  4. Splicing, SNPs located at exonic splicing enhancer (ESE) or exonic splicing silencer (ESS);
  5. 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/)