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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/)