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Table 3 Top 50 candidate SNPs possibly associated with nicotine dependence (CPD)

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(CPD > 20) Genotypeb(CPD ≤ 20) χ2 p Related gene Region MAF TFBS Splicing Polyphen
1 2 rs726016 234390241 0/21/15 0/20/92 22.29 2.35E-06 LOC339766 non-syna 0.13851351 - + probablydamaging
2 2 rs960615 151441447 4/20/12 3/25/84 20.45 6.11E-06 LOC727840 3′ flanking 0.19932432 - - -
3 2 rs11683427 127673013 1/10/25 0/5/107 19.71 9.00E-06 CYP27C1 intron 0.05743243 - - -
4 17 rs4077548 75345351 8/25/3 10/44/57 19.14 1.21E-05 ENPP7 3′ flanking 0.35714286 - - -
5 7 rs2888674 150141848 3/22/11 1/34/77 18.94 1.35E-05 TMEM176A 3′ flanking 0.21621622 - - -
6 7 rs4721629 17542242 1/17/18 0/18/94 18.26 1.93E-05 AHR 3′ flanking 0.125 - - -
7 15 rs10518761 54535156 0/9/27 0/3/109 18.22 1.97E-05 UNC13C intron 0.04054054 - - -
8 18 rs8093458 65163508 7/20/9 2/47/62 17.45 2.94E-05 DOK6 5′ flanking 0.28911565 - - -
9 21 rs8127336 27297806 3/12/21 0/15/97 17.08 3.59E-05 ADAMTS5 5′ flanking 0.11148649 - - -
10 10 rs10904919 17374751 0/18/18 0/18/94 17.04 3.67E-05 ST8SIA6 3′ flanking 0.12162162 - - -
11 7 rs12540772 150160296 6/20/10 3/40/69 16.8 4.16E-05 ABP1 5′ flanking 0.26351351 - - -
12 2 rs1542604 131309515 3/14/19 1/17/94 16.35 5.26E-05 LOC730032 5′ flanking 0.13175676 + - -
13 1 rs10494797 197762985 6/16/14 2/33/77 15.39 8.75E-05 LOC647202 3′ flanking 0.21959459 - - -
14 1 rs6683501 197753037 6/15/15 0/36/76 15.37 8.84E-05 LOC647202 3′ flanking 0.21283784 - - -
15 20 rs4811238 36491682 0/0/36 1/36/75 15.35 8.95E-05 CTNNBL1 intron 0.12837838 - - -
16 7 rs11772167 150134012 2/13/21 0/16/96 14.76 1.22E-04 TMEM176A 3′ flanking 0.11148649 + - -
17 21 rs8126747 41902438 7/18/11 5/37/70 14.59 1.33E-04 TMPRSS2 5′ flanking 0.26689189 - - -
18 15 rs1434462 77306926 0/8/28 11/54/47 14.4 1.48E-04 LOC646956 5′ flanking 0.28378378 - - -
19 7 rs9792016 13823760 7/19/10 7/35/70 14.34 1.53E-04 LOC646161 5′ flanking 0.27702703 - - -
20 21 rs2830596 27276913 7/19/10 5/41/66 14.22 1.62E-04 ADAMTS5 5′ flanking 0.28378378 - - -
21 2 rs11902906 143299978 3/13/20 26/63/23 14.21 1.64E-04 KYNU 5′ flanking 0.4527027 - - -
22 1 rs6658450 197694872 6/17/13 2/38/72 14.12 1.72E-04 LOC647202 3′ flanking 0.23986486 - - -
23 1 rs1416127 56265694 1/20/15 0/29/83 14.12 1.72E-04 LOC127406 3′ flanking 0.1722973 - - -
24 14 rs799045 81687929 5/9/22 33/54/25 14.11 1.72E-04 LOC730103 5′ flanking 0.46959459 - - -
25 7 rs3814991 18601428 10/21/5 12/48/52 14.03 1.80E-04 HDAC9 intron 0.38175676 - - -
26 4 rs7659741 130342701 10/18/8 6/54/52 13.93 1.90E-04 LOC391697 5′ flanking 0.35135135 - - -
27 10 rs1570937 18798899 0/11/24 0/8/103 13.79 2.04E-04 CACNB2 intron 0.06506849 - - -
28 4 rs13435610 181024788 2/17/17 0/26/86 13.79 2.05E-04 LOC643179 3′ flanking 0.15878378 - - -
29 12 rs11613339 39239162 1/16/19 0/20/92 13.77 2.06E-04 NULL intron 0.12837838 - - -
30 6 rs4305747 132959305 0/17/19 21/63/28 13.76 2.08E-04 TAAR5 5′ flanking 0.41216216 + - -
31 8 rs7006843 117669783 0/7/29 10/51/51 13.69 2.16E-04 EIF3H 3′ flanking 0.26351351 - - -
32 11 rs3107636 122287366 4/18/14 4/26/82 13.68 2.17E-04 C11orf63 intron 0.2027027 - - -
33 3 rs13085035 30763983 3/18/15 1/30/81 13.67 2.18E-04 GADL1 intron 0.18918919 - - -
34 2 rs2698537 64363458 1/12/23 0/12/100 13.66 2.19E-04 LOC130773 3′ flanking 0.08783784 - - -
35 19 rs4926219 14441328 2/11/23 0/13/99 13.64 2.21E-04 PKN1 non-syna 0.09459459 - + benign
36 3 rs1157438 22343099 9/14/13 3/43/66 13.54 2.33E-04 LOC728516 3′ flanking 0.27364865 - - -
37 7 rs6980179 150156343 9/20/7 8/50/54 13.5 2.38E-04 TMEM176A 3′ flanking 0.35135135 - - -
38 1 rs10518473 74924774 1/9/26 0/7/105 13.37 2.55E-04 C1orf173 5′ flanking 0.06081081 - - -
39 4 rs4616770 130292102 11/13/12 4/49/59 13.35 2.58E-04 LOC391697 5′ flanking 0.31081081 - - -
40 3 rs2337708 18169752 0/11/25 0/8/104 13.35 2.59E-04 SATB1 3′ flanking 0.06418919 - - -
41 1 rs17461925 201293214 5/14/17 1/29/82 13.16 2.86E-04 PPFIA4 intron 0.18581081 - - -
42 2 rs4851890 98164176 6/18/12 3/40/69 13.1 2.95E-04 VWA3B intron 0.25675676 - - -
43 2 rs6759709 2026404 0/2/34 5/38/69 13.01 3.09E-04 MYT1L intron 0.16891892 - - -
44 18 rs1567041 4485320 16/12/8 14/52/46 12.99 3.14E-04 LOC388458 5′ flanking 0.41891892 - - -
45 3 rs149863 138965053 4/12/20 0/23/89 12.84 3.39E-04 SOX14 5′ flanking 0.14527027 + - -
46 11 rs7945313 91134747 12/12/12 5/50/57 12.83 3.41E-04 LOC727998 3′ flanking 0.32432432 - - -
47 19 rs10417021 62642189 0/12/24 0/10/102 12.82 3.43E-04 ZNF749 5′ flanking 0.07432432 - - -
48 25 rs5988531 884198 2/21/13 2/32/78 12.79 3.48E-04 SHOX | CRLF2 intergenic 0.20608108 not available not available not available
49 4 rs17051378 122785148 8/17/11 4/46/62 12.72 3.62E-04 ANXA5 3′ flanking 0.29391892 - - -
50 11 rs4756986 19056814 7/15/14 4/34/74 12.68 3.69E-04 MRGPRX2 5′ flanking 0.23986486 - - -
  1. CHR, chromosome number; Position, chromosomal position (bp); Related gene, the nearest gene from the SNP site;
  2. a, coding region (nonsynonymous 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/)