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Table 2 Genotype distributions of all tag SNPS in case-control set 1 and the eligible ones in sets 1 and 2 combined

From: Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk

   

Set 1

Sets 1 and 2

SNP

MAF

Base change

Controls

Cases

Odds ratio (95 percent CI)

HWE p value

Genotype frequency p value

Trend test p value

Controls

Cases

Odds ratio (95 percent CI)

Trend test p value

ATM

  

GG

1,881

1,808

1a

       

   ATM-04

0.09

GT

378

364

1.00 [0.86–1.17]

0.84

0.84

0.79

    

   rs4987876

 

TT

18

21

1.21 [0.64–2.29]

       
  

AA

707

694

1a

       

   ATM-05

0.44

AG

1,146

1,069

0.95 [0.83–1.09]

0.24

0.52

0.84

    

   rs189037

 

GG

420

427

1.04 [0.87–1.23]

       
  

AA

2,103

1,992

1a

       

   ATM-06

0.04

AG

169

183

1.14 [0.92–1.42]

0.19

0.47

0.29

    

   rs2234996

 

GG

6

5

0.88 [0.27–2.89]

       
  

AA

727

713

1a

       

   ATM-07

0.43

AG

1,147

1,058

0.94 [0.82–1.07]

0.14

0.37

0.80

    

   rs599164

 

GG

398

409

1.05 [0.88–1.24]

       
  

AA

1,627

1,611

1a

   

3,280

3,223

1a

 

   ATM-08

0.15

AG

606

553

0.92 [0.81–1.05]

0.03

0.09

0.06

1,193

1,081

0.92 [0.84–1.01]

0.10

   rs3092991

 

GG

44

27

0.62 [0.38–1.01]

   

82

74

0.92 [0.67–1.26]

 
  

GG

1,052

990

1a

       

   ATM-09

0.32

GA

1,000

971

1.03 [0.91–1.17]

0.48

0.70

0.41

    

   rs665293

 

AA

222

227

1.09 [0.89–1.33]

       
  

TT

712

688

1a

       

   ATM-10

0.43

TA

1,110

1,036

0.97 [0.84–1.11]

0.45

0.34

0.45

    

   rs582157

 

AA

405

426

1.09 [0.92–1.29]

       
  

CC

2,043

1,990

1a

       

   ATM-11

0.05

CT

214

183

0.88 [0.71–1.08]

0.01

0.35

0.15

    

   rs1800889

 

TT

13

9

0.71 [0.30–1.67]

       
  

GG

1,945

1,872

1a

       

   ATM-12

0.08

GA

310

300

1.01 [0.85–1.19]

0.02

0.48

0.64

    

   rs611018

 

AA

22

14

0.66 [0.34–1.30]

       

BRCA1

   P871l

 

TT

1,001

939

1a

       

   BRCA1-01

0.33

TC

1,031

996

1.03 [0.91–1.17]

0.19

0.40

0.22

    

   rs1799917

 

CC

234

252

1.15 [0.94–1.40]

       

   Q356R

 

TT

2,004

1,955

1a

   

4,013

3,879

1a

 

   BRCA1-02

0.06

TC

256

221

0.89 [0.73–1.07]

0.13

0.15

0.08

511

469

0.95 [0.83–1.08]

0.23

   rs1799950

 

CC

13

6

0.47 [0.18–1.25]

   

23

14

0.63 [0.32–1.23]

 
  

TT

1,673

1,580

1a

       

   BRCA1-05

0.14

TC

553

568

1.09 [0.95–1.25]

0.87

0.45

0.38

    

   rs8176166

 

CC

47

42

0.95 [0.62–1.44]

       
  

TT

1,281

1,208

1a

       

   BRCA1-06

0.25

TG

857

851

1.05 [0.93–1.19]

0.69

0.68

0.65

    

   rs8176199

 

GG

137

127

0.95 [0.76–1.27]

       
  

GG

1,893

1,834

1a

       

   BRCA1-07

0.09

GA

362

337

0.96 [0.82–1.13]

0.31

0.53

0.38

    

   rs3737559

 

AA

22

15

0.70 [0.36–1.36]

       

BRCA2

  

TT

715

688

1a

       

   BRCA2-01

0.45

TC

1,083

1,057

1.01 [0.89–1.16]

0.08

0.72

0.62

    

   rs206115

 

CC

475

435

0.95 [0.81–1.13]

       
  

GG

870

813

1a

   

1,676

1,621

1a

 

   BRCA2-02

0.39

GA

1020

1,010

1.06 [0.93–1.21]

0.39

0.63

0.79

2,145

2,028

0.98 [0.89–1.07]

0.95

   rs206116

 

AA

380

355

1.00 [0.84–1.19]

   

724

705

1.01 [0.89–1.14]

 
  

GG

1,576

1,504

1a

       

   BRCA2-03

0.17

GA

628

601

1.00 [0.88–1.15]

0.96

0.64

0.58

    

   rs3092989

 

AA

63

71

1.18 [0.83–1.67]

       
  

AA

1,515

1,506

1a

   

3,046

2,943

1a

 

   BRCA2-04

0.19

GA

667

616

0.93 [0.81–1.06]

0.07

0.02

0.02

1,328

1,287

1.00 [0.92–1.10]

0.29

   rs206118

 

GG

91

57

0.63 [0.45–0.88]

   

172

132

0.79 [0.63–1.00]

 
  

AA

1,353

1,241

1a

   

2,691

2,502

1a

 

   BRCA2-05

0.22

GA

763

719

1.03 [0.90–1.17]

0.09

0.75

0.98

1,594

1,486

1.00 [0.92–1.10]

0.40

   rs206119

 

GG

102

86

0.92 [0.68–1.24]

   

203

216

1.14 [0.94–1.40]

 
  

GG

1,263

1,189

1a

       

   BRCA2-07

0.25

GT

875

828

1.01 [0.89–1.14]

0.31

0.21

0.23

    

   rs9567552

 

TT

135

158

1.24 [0.98–1.59]

       
  

GG

612

626

1a

   

1,228

1,200

1a

 

   BRCA2-09

0.48

GA

1,137

1,082

0.93 [0.81–1.07]

0.46

0.22

0.08

2,317

2,189

0.97 [0.88–1.07]

0.60

   rs9534174

 

AA

523

461

0.86 [0.72–1.02]

   

1,006

954

0.97 [0.86–1.09]

 
  

CC

1,487

1,453

1a

       

   BRCA2-10

0.18

CT

669

620

0.95 [0.83–1.08]

0.62

0.63

0.73

    

   rs2126042

 

TT

70

74

1.08 [0.77–1.51]

       
  

AA

1,824

1,701

1a

   

3,609

3,434

1a

 

   BRCA2-11

0.10

AC

428

450

1.13 [0.97–1.31]

0.40

0.10

0.04

893

876

1.03 [0.92–1.14]

0.28

   rs11571686

 

CC

25

35

1.50 [0.89–2.52]

   

52

63

1.27 [0.88–1.84]

 
  

AA

1,422

1,290

1a

   

2,812

2,672

1a

 

   BRCA2-13

0.21

AG

761

776

1.12 [0.99–1.27]

0.70

0.03

0.01

1,548

1,491

1.01 [0.93–1.11]

0.48

   rs1799955

 

GG

92

115

1.38 [1.04–1.83]

   

194

201

1.09 [0.89–1.34]

 
  

GG

1,204

1,205

1a

       

   BRCA2-14

0.27

GA

907

833

0.92 [0.81–1.04]

0.83

0.26

0.10

    

   rs1151742

 

AA

167

145

0.87 [0.68–1.10]

       
  

AA

1,733

1,603

1a

       

   BRCA2-16

0.12

AG

484

414

0.92 [0.80–1.07]

0.33

0.56

0.43

    

   rs4942485

 

GG

34

33

1.05 [0.65–1.70]

       
  

CC

2,020

1,910

1a

       

   BRCA2-18

0.06

CA

235

253

1.14 [0.94–1.38]

6 × 10-5

0.27

0.11

    

   rs11571789

 

AA

19

24

1.34 [0.73–2.45]

       
  

AA

1,247

1,186

1a

       

   BRCA2-19

0.26

AG

829

820

1.04 [0.92–1.18]

0.11

0.83

0.63

    

   rs542551

 

GG

164

159

1.02 [0.81–1.29]

       
  

AA

1,383

1,370

1a

   

2,791

2,668

1a

 

   BRCA2-21

0.22

AG

769

720

0.94 [0.83–1.07]

0.39

0.15

0.08

1,527

1,465

1.00 [0.92–1.10]

0.54

   rs206343

 

GG

119

90

0.76 [0.57–1.01]

   

225

192

0.89 [0.73–1.09]

 

   N372H

 

AA

1,149

1,109

1a

   

2,306

2,182

1a

 

   BRCA2-22

0.28

AC

942

896

0.98 [0.87–1.11]

0.07

0.96

0.78

1,892

1,824

1.02 [0.93–1.11]

0.58

   rs144848

 

CC

171

161

0.97 [0.77–1.23]

   

339

333

1.04 [0.88–1.22]

 

CHEK2

  

AA

914

857

1a

       

   CHEK2-05

0.37

AT

1,045

1,019

1.04 [0.92–1.18]

0.55

0.82

0.60

    

   rs5762760

 

TT

315

306

1.04 [0.86–1.24]

       
  

AA

1,296

1,243

1a

       

   CHEK2-06

0.25

AG

813

789

1.01 [0.89–1.15]

0.11

0.72

0.72

    

   rs2073327

 

GG

152

133

0.91 [0.71–1.17]

       
  

GG

1,554

1,548

1a

       

   CHEK2-07

0.17

GC

633

558

0.88 [0.77–1.01]

0.87

0.20

0.12

    

   rs2347443

 

CC

66

62

0.94 [0.66–1.34]

       
  

GG

1,150

1,130

1a

       

   CHEK2-08

0.29

GA

938

868

0.94 [0.83–1.07]

0.63

0.64

0.50

    

   rs738722

 

AA

182

175

0.98 [0.78–1.22]

       
  

GG

1,718

1,598

1a

   

3,439

3,199

1a

 

   CHEK2-09

0.13

GA

510

553

1.17 [1.02–1.34]

0.31

0.04

0.18

1,021

1,087

1.14 [1.04–1.26]

0.07

   rs2236141

 

AA

41

29

0.76 [0.47–1.23]

   

86

69

0.86 [0.63–1.19]

 
  

GG

1,235

1,198

1a

       

   CHEK2-10

0.26

GA

872

834

0.99 [0.87–1.12]

0.55

0.76

0.54

    

   rs4035540

 

AA

144

127

0.91 [0.71–1.17]

       
  

AA

1,914

1,885

1a

   

3,866

3,770

1a

 

   CHEK2-11

0.08

AT

331

281

0.86 [0.73–1.02]

0.71

0.22

0.10

633

563

0.91 [0.81–1.03]

0.11

   rs1076807

 

TT

17

15

0.90 [0.45–1.80]

   

28

23

0.84 [0.48–1.46]

 
  

GG

1,150

1,130

1a

       

   CHEK2-12

0.29

GA

928

851

0.93 [0.82–1.06]

0.87

0.54

0.47

    

   rs1807609

 

AA

184

178

0.98 [0.79–1.23]

       
  

GG

1,992

1,886

1a

       

   CHEK2-13

0.06

GA

270

2,866

1.12 [0.94–1.34]

0.19

0.38

0.17

    

   rs17508019

 

AA

5

7

1.48 [0.47–4.67]

       
  

CC

694

626

1a

   

1,410

1,249

1a

 

   CHEK2-14

0.45

CG

1,114

1,057

1.05 [0.92–1.21]

0.09

0.18

0.07

2,188

2,123

1.10 [0.99–1.21]

0.02

   rs9608698

 

GG

463

488

1.17 [0.99–1.38]

   

940

956

1.15 [1.02–1.29]

 

   1100delCb

0.02

CC

    

0.90

 

2,887

2,671

1a

0.002

  

delC

      

14

34

2.63 [1.41–4.90]

 

TP53

   R72P

 

GG

1,177

1,107

1a

       

   TP53-01

0.27

GC

854

768

0.96 [0.84–1.09]

0.52

0.75

0.48

    

   rs1042522

 

CC

166

148

0.95 [0.75–1.20]

       
  

CC

1,622

1,545

1a

       

   TP53-02

0.14

CT

520

449

0.91 [0.79–1.05]

0.09

0.39

0.20

    

   rs1625895

 

TT

55

48

0.92 [0.62–1.36]

       
  

CC

1,797

1,699

1a

       

   TP53-03

0.11

CG

438

453

1.09 [0.94–1.27]

0.04

0.45

0.41

    

   rs2287499

 

GG

39

34

0.92 [0.58–1.47]

       
  

AA

2,053

1,971

1a

       

   TP53-06

0.05

AG

217

204

0.98 [0.80–1.20]

0.77

0.91

0.94

    

   rs17887200

 

GG

5

6

1.25 [0.38–4.10]

       
  

CC

2,067

1,986

1a

       

   TP53-07

0.05

CT

204

198

1.01 [0.82–1.24]

0.99

0.81

0.76

    

   rs17886760

 

TT

5

7

1.46 [0.46–4.60]

       
  

CC

865

833

1a

       

   TP53-08

0.39

CT

1,069

1,022

0.99 [0.87–1.13]

0.69

0.95

0.89

    

   rs9893249

 

TT

342

336

1.02 [0.84–1.22]

       
  1. Values in the minor allele frequency (MAF) and Hardy-Weinberg equilibrium (HWE) p value columns refer to controls only. aReference group. bAttempted in only 61% of subjects. CI, confidence interval.