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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/)
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Molecular Brain

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