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Table 1 Genes that contain overlapping clusters of nominally positive SNPs in both ECA and European-American MNB research volunteer samples that display nominal p < 0.05.

From: Genome wide association for substance dependence: convergent results from epidemiologic and research volunteer samples

    

Clust SNPs

 

gene

ch

bp

description

ECA

MNB

p

A2BP1

16

6,009,133

ataxin 2-binding protein 1

16

42

0.0038

ACCN1

17

28,364,218

neuronal amiloride-sens cation chan 1

5

5

0.0240

ADARB2

10

1,218,073

RNA spec A deaminase B2

4

8

0.0420

ADCY2

5

7,449,345

adenylate cyclase 2

7

6

0.0210

AGBL4

1

48,822,129

ATP/GTP binding protein-like 4

3

8

0.0400

AK5

1

77,520,330

adenylate kinase 5

10

4

0.0090

AKAP6

14

31,868,274

A kinase anchoring protein 6

3

15

0.0210

ALK

2

29,269,144

anaplastic lymphoma kinase (Ki-1)

6

10

0.0470

ANKFN1

17

51,585,835

ankyrin-rep Fn III dom cont 1

3

14

0.0130

ATXN1

6

16,407,322

ataxin 1

3

17

0.0120

C18orf1

18

13,208,795

chromosome 18 open reading frame 1

4

6

0.0440

C3orf21

3

196,270,302

chromosome 3 open reading frame 21

4

4

0.0380

C8A

1

57,093,065

complement component 8 α polypep

3

7

0.0180

C9orf88

9

129,307,439

Chr 9 open reading frame 88

4

4

0.0220

CABIN1

22

22,737,765

calcineurin binding protein 1

4

4

0.0220

CACNA2D3

3

54,131,733

voltage det Ca chan α2/δ3 subunit

12

18

0.0091

CCBE1

18

55,252,124

collagen and calcium binding EGF domains 1

7

10

0.0090

CCDC63

12

109,769,194

coiled-coil domain containing 63

3

4

0.0290

CD180

5

66,513,872

CD180 molecule

5

5

0.0051

CDH13

16

81,218,079

cadherin 13

18

65

0.0019

CDH23

10

72,826,697

cadherin-like 23

7

4

0.0380

CGNL1

15

55,455,997

cingulin-like 1

3

11

0.0040

CHL1

3

213,650

close homolog of L1

3

12

0.0103

CHST11

12

103,370,614

chondroitin 4 sulfotransferase 11

4

4

0.0470

CIT

12

118,607,981

citron rho-interacting, serine/threonine kinase 21

5

6

0.0160

CNTN5

11

98,397,081

contactin 5

11

10

0.0390

CNTNAP2

7

145,444,386

contactin associated protein-like 2

22

9

0.0380

CPVL

7

29,001,772

carboxypeptidase vitellogenic-like

4

4

0.0290

CRYL1

13

19,875,810

crystalline λ1

4

5

0.0170

CSMD1

8

2,782,789

CUB and Sushi multiple domains 1

29

137

0.0014

CUGBP2

10

11,087,290

CUG triplet repeat RNA bind prot 2

16

4

0.0031

DAB1

1

57,236,167

disabled homolog 1

4

24

0.0140

DLC1

8

12,985,243

deleted in liver cancer 1

13

9

0.0059

DNAPTP6

2

200,879,041

DNA polymerase-transactivated protein 6

8

4

0.0140

DOCK2

5

168,996,871

dedicator of cytokinesis 2

3

7

0.0490

DPP6

7

154,060,464

dipeptidyl-peptidase 6

6

4

0.0250

EDNRA

4

148,621,575

endothelin receptor type A

3

4

0.0280

EFCAB4B

12

3,627,370

EF-hand calcium binding domain 4B

3

6

0.0165

EPHB1

3

135,996,950

EPH receptor B1

13

5

0.0090

ESRRG

1

214,743,211

estrogen-related receptor γ

3

14

0.0210

EVI1

3

170,285,244

ecotropic viral integration site 1

3

12

0.0047

F5

1

167,750,033

coagulation factor V

4

11

0.0049

FAM13A1

4

89,866,129

family with seq sim 13 A1

6

4

0.0360

FAM3C

7

120,776,141

family with sequence similarity 3 C

6

4

0.0109

FAM3D

3

58,594,710

family with sequence similarity 3 D

7

4

0.0063

FBXL17

5

107,223,348

F-box and leucine-rich repeat protein 17

6

6

0.0430

FGD2

6

37,081,401

FYVE, RhoGEF PH dom cont 2

3

4

0.0320

FHIT

3

59,710,076

fragile histidine triad gene

24

62

0.0030

FLJ11151

16

12,664,438

hypothetical protein FLJ11151

4

4

0.0380

FLJ32682

13

45,013,433

hypothetical protein FLJ32682

4

5

0.0180

FN1

2

215,933,422

fibronectin 1

3

5

0.0260

FOXP1

3

71,087,426

forkhead box P1

4

17

0.0180

FREM3

4

144,717,905

FRAS1 related extracellular matrix 3

4

6

0.0130

FRMD4A

10

13,725,718

FERM domain containing 4A

3

23

0.0090

GABBR2

9

100,090,187

GABA B receptor 2

11

6

0.0073

GLIS3

9

3,817,676

GLIS family zinc finger 3

13

18

0.0016

GRB10

7

50,625,259

growth factor receptor-bound protein 10

3

13

0.0083

GRID1

10

87,349,292

delta 1 inotropic glutamate rec

7

18

0.0130

GRIK1

21

29,831,125

kainate 1 inotropic glutamate rec

4

12

0.0150

GTF2F2L

4

148,646,691

general transcription fact IIFpolypep 2-L

3

3

0.0170

HPSE2

10

100,208,867

heparanase 2

6

18

0.0160

HS3ST4

16

25,611,240

heparan sulfate 3-O-sulfotransferase 4

4

11

0.0250

IMPA2

18

11,971,455

inositol(myo)-1(or 4)-monophosphatase 2

6

6

0.0064

IQGAP2

5

75,734,905

IQ motif cont GTPase activ prot 2

7

5

0.0170

JAKMIP1

4

6,106,385

janus kinase microtubule interacting protein 1

3

8

0.0138

KCNB1

20

47,421,912

Shab-rel volt-gated K chan 1

5

3

0.0190

KCNIP4

4

20,339,337

Kv channel interacting protein 4

13

9

0.0107

KCNJ6

21

37,918,655

inwardly-rect K chan J 6

3

8

0.0330

KCNMA1

10

78,299,366

large conduct Ca-act K chan M α1

8

8

0.0390

KIAA1576

16

76,379,984

KIAA1576 protein

3

6

0.0260

KREMEN1

22

27,799,106

kringle cont TM prot 1

5

4

0.0190

KSR2

12

116,389,387

kinase suppressor of ras 2

5

4

0.0430

LDLRAD3

11

35,922,188

low density lipoprotein recep cl A dom cont 3

3

6

0.0330

LTF

3

46,452,500

lactotransferrin

3

4

0.0290

MAGI1

3

65,314,946

membr-assoc G kinase WW PDZ dom cont 1

6

9

0.0380

MAGI2

7

77,484,310

membrane assoc G kinase WW PDZ dom 2

9

16

0.0430

MGC23985

5

147,252,464

similar to AVLV472

3

7

0.0085

MICAL2

11

12,088,714

calponin LIM cont microtub monoxygenase 2

8

8

0.0120

MTSS1

8

125,632,212

metastasis suppressor 1

9

9

0.0050

MTUS1

8

17,545,583

mitochondrial tumor suppressor 1

3

4

0.0090

MYO18B

22

24,468,120

myosin XVIIIB

15

8

0.0460

MYO3A

10

26,263,202

myosin IIIA

3

5

0.0018

NAALADL2

3

176,059,805

N-Ac α-linked acidic dipeptidase-L 2

4

5

0.0340

NFIA

1

61,320,881

nuclear factor I/A

4

4

0.0080

NLGN1

3

174,598,938

neuroligin 1

4

4

0.0260

OPCML

11

131,790,085

opioid binding protein/cell adhesion molecule-L

10

13

0.0076

PALM2

9

111,442,893

paralemmin 2

10

16

0.0220

PALM2-AKAP2

9

111,582,410

PALM2-AKAP2 protein

5

10

0.0021

PARD3B

2

205,118,761

par-3 partitioning defective 3 homolog B

3

5

0.0160

PDE4D

5

58,302,468

cAMP spec phosphodiesterase 4D

4

4

0.0140

PKD1L2

16

79,691,991

polycystic kidney disease 1-like 2

4

4

0.0060

PLD5

1

240,318,895

phospholipase D family 5

3

16

0.0300

PRKCA

17

61,729,388

protein kinase C α

6

4

0.0113

PRKCH

14

60,858,268

protein kinase C η

7

22

0.0300

PRKG1

10

52,504,299

cGMP dep protein kinase I

12

10

0.0014

PRPF4

9

115,077,795

PRP4 pre-mRNA process fact 4 homol

6

4

0.0360

PSD3

8

18,432,343

pleckstrin and Sec7 domain containing 3

8

16

0.0240

PTPN14

1

212,597,634

no rec prot Y phosphatase 14

10

4

0.0150

PTPRK

6

128,331,625

recept protein tyrosine phosphatase K

3

8

0.0062

PTPRT

20

40,134,806

recept prot Y phosphatase T

3

15

0.0190

RBMS3

3

29,297,947

sing strand RNA binding motif interact prot

5

13

0.0230

ROR2

9

93,524,705

receptor tyrosine kinase-L orphan recept 2

5

4

0.0290

RORA

15

58,576,755

RAR-related orphan receptor A

4

9

0.0220

SLC2A13

12

38,435,090

solute carrier family 2 13

4

4

0.0086

SLIT3

5

168,025,857

slit homolog 3

3

4

0.0370

SRGAP3

3

8,997,278

SLIT-ROBO Rho GTPase activating protein 3

4

23

0.0087

STK32B

4

5,104,428

serine threonine kinase 32B

3

25

0.0011

STK39

2

168,518,777

serine threonine kinase 39

4

4

0.0036

SYNE1

6

152,484,516

spectrin rep cont nuclear envelope 1

7

5

0.0034

TACC2

10

123,738,679

transforming acidic coil-coil cont prot 2

3

9

0.0430

TBC1D22A

22

45,537,213

TBC1 domain family 22A

3

8

0.0270

TEK

9

27,099,286

TEK tyrosine kinase, endothelial

3

9

0.0420

TG

8

133,948,387

thyroglobulin

4

4

0.0180

THSD4

15

69,220,842

thrombospondin I dom cont 4

3

11

0.0063

TMEM132C

12

127,318,855

transmembrane protein 132C

5

13

0.0084

TMEM132D

12

128,122,224

transmembrane protein 132D

8

11

0.0090

TMEM16D

12

99,712,716

transmembrane protein 16D

11

11

0.0320

TMTC1

12

29,545,024

transmemb tetratricopep rep cont 1

3

3

0.0035

TRPC4

13

37,108,795

transient receptor potential cation channel C 4

8

4

0.0140

TULP4

6

158,653,680

tubby like protein 4

6

9

0.0076

UNC5C

4

96,308,712

unc-5 homolog C

9

4

0.0162

VAMP4

1

169,938,783

vesicle-associated membrane protein 4

3

5

0.0170

VAPB

20

56,397,651

vesicle-assoc memb protein-assoc prot B C

4

11

0.0034

VIT

2

36,777,418

Vitrin

3

9

0.0110

ZNF365

10

63,803,957

zinc finger protein 365

6

4

0.0340

ZNF406

8

135,559,213

zinc finger protein 406

16

4

0.0014

  1. The numbers of nominally-positive SNPs that lay in clusters within the gene's exons and in 10 kb genomic flanking regions are noted for each sample. Chromosome number and initial chromosomal position for the cluster (bp, NCBI Mapviewer Build 36.1) are listed. Nominal p values for each gene are based on 10,000 Monte Carlo simulation trials. For each trial, the number of times randomly-selected segments of the genome that lie within genes are assessed for the same features displayed by the actual gene identified. Note that the very highly significant p values for the overall convergence noted between these two datasets (text) does account for multiple comparisons, while the much more modest p values for many of the individual genes (displayed here) do not. Genes that are identified by clustered nominally positive SNPs in both samples but whose gene-wise p values lie > 0.05 (perhaps, in part, due to the large size of the genes) include: C4orf13, PRKCE, UNC13C, KIAA1303, MYR8, DNAH11, ONECUT2, TGFBR3, TPD52L1, C9orf28, TMEM108, GALNT14, HECW2, NFIB, STS-1, KIAA1217, RAB3C, SNTG1, CPNE4, PTPRM, SLC39A11, MDS1, GPC5, ZNF533, NR5A2, RYR3, C8orf68, CTNNA2, GRM5, ATRNL1, ARL15, BTBD9, CNTNAP5, GALNTL4, PELI2, SNRPN, GPR98, ERC2, NFATC2, FLJ16124, GRM7, SORCS2, NPAS3, PARVB, IGL@ and LRP1B.