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Table 2 Top candidate SNPs selected after final stage analysis in 3-stage GWAS targeting all SNPs (hypoesthesia)

From: Genome-wide association study of sensory disturbances in the inferior alveolar nerve after bilateral sagittal split ramus osteotomy

Model

Rank

SNP

CHR

Position

1st stage

2nd stage

Final stage

Combined

Genotype

Related gene

     

X 2

P

X 2

P

X 2

P

Q

X 2

P

Abnormal

Normal

 

Trend

1

rs7228266

18

40874531

4.377

0.0364

6.005

0.0143

9.102

0.0026

0.567

19.15

1.21E-05

7/28/16

8/92/153

SETBP1

Trend

2

rs6537883

1

110206794

5.962

0.0146

5.917

0.015

6.385

0.0115

0.6855

18.13

2.06E-05

2/6/43

35/93/121

CSF1

Trend

3

rs9474312

6

52706460

5.95

0.0147

6.026

0.0141

5.866

0.0154

0.6855

18.03

2.18E-05

9/24/18

11/84/157

LOC730152

Trend

4

rs1870761

11

122356773

4.184

0.0408

7.947

0.0048

4.011

0.0452

0.7696

15.87

6.79E-05

0/8/42

16/100/134

BSX

Trend

5

rs139131

22

42912379

7.103

0.0077

4.071

0.0436

4.38

0.0364

0.7696

15.6

7.81E-05

0/7/44

10/100/143

PARVG

Trend

6

rs2295343

20

3683601

4.657

0.0309

4.81

0.0283

6.327

0.0119

0.6855

15.11

0.000101

0/6/45

10/93/150

C20orf27

Dominant

1

rs6537883

1

110206794

7.505

0.0062

5.984

0.0144

8.612

0.0033

0.4897

21.79

3.04E-06

2/6/43

35/93/121

CSF1

Dominant

2

rs139131

22

42912379

7.32

0.0068

4.126

0.0422

4.264

0.0389

0.763

15.87

6.78E-05

0/7/44

10/100/143

PARVG

Dominant

3

rs2295343

20

3683601

4.574

0.0325

5.147

0.0233

6.631

0.01

0.5288

15.46

8.41E-05

0/6/45

10/93/150

C20orf27

Dominant

4

rs10502849

18

40866089

5.286

0.0215

3.933

0.0473

6.161

0.0131

0.5288

15.25

9.41E-05

11/28/11

20/101/1

SETBP1

Dominant

5

rs707816

6

13742961

4.586

0.0322

3.933

0.0473

5.075

0.0243

0.7257

13.08

0.000299

2/15/34

33/121/99

RANBP9

Recessive

1

rs2817461

6

156954704

8.06

0.0045

12.55

0.0004

12.53

0.0004

0.0521

30.33

3.64E-08

9/42

3/250

ARID1B

Recessive

2

rs502281

6

156910640

3.991

0.0458

6.935

0.0085

16.44

5E-05

0.0196*

24.72

6.63E-07

7/9/35

2/71/180

ARID1B

Recessive

3

rs2063640

3

103685735

6.085

0.0136

4.932

0.0264

14.38

0.0001

0.0291*

23.07

1.56E-06

15/11/25

17/110/125

ZPLD1

Recessive

4

rs13236243

7

17284837

10.43

0.0012

6.658

0.0099

4.14

0.0419

0.7421

21.14

4.28E-06

16/16/19

21/121/111

LOC729939

Recessive

5

rs1054611

12

10061428

6.1

0.0135

4.344

0.0371

11.07

0.0009

0.0775

20.61

5.64E-06

10/16/25

8/84/161

CLEC12B

Recessive

6

rs6833812

4

5161041

3.991

0.0458

12.25

0.0005

5.428

0.0198

0.4066

20.11

7.32E-06

4/9/38

0/57/196

STK32B

Recessive

7

rs1059513

12

55775976

8.06

0.0045

6.062

0.0138

5.428

0.0198

0.4066

20.11

7.32E-06

4/8/39

0/32/221

STAT6

Recessive

8

rs1998930

6

156945948

5.157

0.0232

11.29

0.0008

6.002

0.0143

0.4066

19.52

9.94E-06

22/21/8

40/130/83

ARID1B

Recessive

9

rs4235662

5

84203580

7.754

0.0054

6.062

0.0138

5.428

0.0198

0.4066

19.42

1.05E-05

5/18/28

1/96/156

EDIL3

Recessive

10

rs3804357

4

102221146

5.165

0.0231

6.551

0.0105

10.84

0.001

0.0775

19.3

1.12E-05

8/16/27

5/102/144

PPP3CA

Recessive

11

rs4732828

8

28050160

3.991

0.0458

5.99

0.0144

5.791

0.0161

0.4066

15.27

9.31E-05

3/5/42

0/20/232

ELP3

Recessive

12

rs4658506

1

240012540

3.991

0.0458

6.062

0.0138

5.428

0.0198

0.4066

15.03

0.000106

3/11/37

0/67/186

WDR64

Recessive

13

rs2868145

19

37738954

3.991

0.0458

6.062

0.0138

5.428

0.0198

0.4066

15.03

0.000106

3/10/38

0/42/211

PDCD5

Recessive

14

rs1564492

15

71720771

3.991

0.0458

6.062

0.0138

5.428

0.0198

0.4066

15.03

0.000106

3/10/38

0/37/216

NPTN

Recessive

15

rs1072056

5

110532014

3.991

0.0458

6.062

0.0138

5.428

0.0198

0.4066

15.03

0.000106

3/6/42

0/59/194

WDR36

Recessive

16

rs10512369

9

109805180

3.991

0.0458

6.062

0.0138

5.428

0.0198

0.4066

15.03

0.000106

3/7/41

0/25/228

LOC392382

Recessive

17

rs10841907

12

21942563

5.185

0.0228

5.026

0.025

4.956

0.026

0.5072

14.95

0.00011

11/18/21

14/104/135

ABCC9

Recessive

18

rs9942977

9

108422182

3.895

0.0484

6.062

0.0138

5.428

0.0198

0.4066

14.91

0.000113

3/5/43

0/28/223

LOC644620

Recessive

19

rs395640

21

26891730

3.991

0.0458

6.062

0.0138

6.074

0.0137

0.4066

14.55

0.000136

4/12/35

1/75/177

CYYR1

Recessive

20

rs13110230

4

178153868

3.991

0.0458

6.062

0.0138

6.074

0.0137

0.4066

14.55

0.000136

4/9/38

1/48/204

VEGFC

Recessive

21

rs1960997

11

97149034

3.991

0.0458

4.344

0.0371

5.675

0.0172

0.4066

11.66

0.000638

6/19/26

5/104/144

CNTN5

Recessive

22

rs9535720

13

51092945

3.999

0.0455

3.907

0.0481

4.141

0.0419

0.7421

11.61

0.000656

6/19/26

38/140/75

WDFY2

  1. CHR, chromosome number; Position, chromosomal position (bp); Q, Q value for FDR correction of multiple comparison; Related gene, the nearest gene from the SNP site; *, Significant after FDR correction (Q < 0.05).