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Table 1 SNP Frequencies and Hardy-Weinberg P-Values

From: The BRCA1 Ashkenazi founder mutations occur on common haplotypes and are not highly correlated with anonymous single nucleotide polymorphisms likely to be used in genome-wide case-control association studies

       

Ashkenazi Jews (n = 85)

CEPH (n = 60)

African Americans (n = 48)

Chinese Americans (n = 48)

Mexican Americans (n = 48)

rs number

SNP Number

SNP name

Position b33a

Position b36.1b

Com Allelec

Min Alleled

mafe

P-value

maf

P-value

maf

P-value

maf

P-value

maf

P-value

13119

1

C_9270420

41373486

38718247

c

t

0.424

0.580

0.350

0.712

0.177

0.624

0.396

0.359

0.458

0.961

748620

2

C_9270421

41373037

38717798

c

g

0.440

0.640

0.350

0.712

0.240

0.550

0.391

0.518

0.465

0.669

17599948

3

C_9270454

41364175

38708936

a

g

0.211

0.649

0.192

0.865

0.104

0.022

0.094

0.326

0.362

0.591

11653231

4

C_95201

41240225

38584986

g

a

0.435

0.703

0.350

0.712

0.240

0.550

0.396

0.359

0.467

0.905

9908805

5

C_3178692

41230675

38575436

c

t

  

0.008

0.948

0.375

0.878

  

0.011

0.941

2175957

6

C_11631183

41195587

38540348

t

g

0.447

0.665

0.350

0.712

0.250

0.441

0.396

0.359

0.446

0.935

3092986

7

BR1_000340

41186761

38531522

a

g

0.051

0.636

0.042

0.736

0.010

0.942

  

0.031

0.823

8176072

8

BR1_000392

41186709

38531470

t

a

0.006 f

0.957

        

8176074

9

BR1_000571

41186530

38531291

g

a

    

0.010

0.942

    

3765640

10

C_2615164

41185012

38529773

a

g

0.440

0.640

0.350

0.712

0.228

0.740

0.394

0.433

0.444

0.592

NAg

11

M_185delAG

41184811

38529572

a

-

0.006

0.957

        

8176090

12

BR1_007918

41179183

38523944

c

g

  

0.008

0.948

0.096

0.338

    

1800062

13

BR1_010574

41176528

38521289

g

a

      

0.021

0.883

  

8176101

14

BR1_010796

41176306

38521067

a

t

    

0.021

0.882

    

8176103

15

C_2615171

41175815

38520576

g

a

0.463

0.291

0.350

0.712

0.234

0.640

0.396

0.359

0.458

0.961

8176104

16

BR1_011340

41175762

38520523

g

a

0.024

0.824

0.033

0.789

    

0.010

0.942

8176109

17

C_2615172

41174541

38519302

a

g

0.441

0.497

0.350

0.712

0.239

0.609

0.396

0.359

0.469

0.751

8065872

18

BR1_016775

41170328

38515089

t

a

    

0.135

0.278

  

0.010

0.942

8176120

19

BR1_017105

41169998

38514759

g

a

0.424

0.913

0.350

0.712

0.240

0.550

0.396

0.359

0.458

0.961

799914

20

BR1_018573

41168546

38513307

g

a

    

0.135

0.278

    

799913

21

BR1_019408

41167711

38512472

a

g

0.032

0.772

0.042

0.736

0.365

0.813

  

0.010

0.942

8176128

22

BR1_019904

41167215

38511976

t

a

    

0.063

0.644

    

8176133

23

BR1_020896

41166223

38510984

t

g

0.422

0.738

0.350

0.712

0.167

0.488

0.396

0.359

0.458

0.961

799912

24

C_2615180

41165899

38510660

c

t

0.472

0.701

0.364

0.926

0.125

0.322

0.396

0.359

0.489

0.882

799923

25

BR1_026422

41160696

38505457

c

t

0.232

0.031

0.308

0.858

0.042

0.763

  

0.104

0.459

8176145

26

BR1_029258

41157859

38502620

t

c

0.400

0.038

0.319

0.586

0.240

0.550

0.404

0.309

0.448

0.829

8176146

27

BR1_029448

41157669

38502430

c

t

0.031

0.774

0.008

0.948

      

7503154

28

BR1_030748

41156369

38501130

t

g

0.415

0.618

0.339

0.478

0.223

0.771

0.396

0.359

0.468

0.862

1799950

29

BR1_031875

41155246

38500007

a

g

0.077

0.442

0.042

0.736

0.010

0.942

  

0.031

0.823

4986850

30

BR1_032885

41154236

38498997

g

a

0.133

0.096

0.113

0.071

0.033

0.819

  

0.013

0.935

16940

31

BR1_033119

41154002

38498763

t

c

0.422

0.429

0.350

0.712

0.177

0.624

0.396

0.359

0.448

0.829

799917

32

BR1_033420

41153701

38498462

c

t

0.429

0.766

0.358

0.868

0.125

0.322

0.396

0.359

0.479

0.571

4986852

33

BR1_003927

41153194

38497955

g

a

0.012

0.912

0.042

0.736

0.010

0.942

    

2227945

34

BR1_034226

41152895

38497656

a

g

    

0.052

0.703

  

0.010

0.942

16942

35

BR1_034356

41152765

38497526

a

g

0.433

0.868

0.348

0.615

0.245

0.521

0.396

0.359

0.447

0.716

799916

36

C_7530109

41151955

38496716

t

g

0.438

0.482

0.358

0.868

0.271

0.703

0.394

0.433

0.479

0.894

2070833

37

BR1_035507

41151614

38496375

c

a

0.031

0.001

    

0.271

0.726

0.135

0.167

2070834

38

BR1_036077

41151050

38495811

a

c

0.435

0.626

0.342

0.568

0.250

1.000

0.396

0.359

0.438

0.634

8176158

39

BR1_036793

41150334

38495095

a

g

0.418

0.393

0.353

0.665

0.174

0.532

0.396

0.359

0.458

0.961

8176160

40

BR1_036859

41150268

38495029

a

g

0.435

0.626

0.350

0.712

0.240

0.550

0.396

0.359

0.458

0.961

8176166

41

BR1_038085

41149042

38493803

a

g

0.196

0.391

0.150

0.172

0.104

0.022

0.120

0.632

0.344

0.395

8176174

42

BR1_040350

41146777

38491538

a

t

    

0.063

0.644

    

3950989

43

C_3178696

41146718

38491479

g

a

0.441

0.566

0.348

0.615

0.234

0.640

0.396

0.359

0.457

0.923

8176175

44

BR1_040669

41146458

38491220

t

-

0.006

0.956

    

0.073

0.586

  

8176177

45

BR1_041288

41145840

38490601

a

g

    

0.021

0.883

    

8176178

46

BR1_041721

41145407

38490168

a

g

    

0.042

0.763

    

1060915

47

C_3178676

41143235

38487996

a

g

0.380

0.105

0.352

0.851

0.177

0.624

0.396

0.359

0.468

0.862

3737559

48

C_3178677

41143069

38487830

c

t

0.124

0.481

0.067

0.580

  

0.083

0.208

0.043

0.761

8176187

49

BR1_045154

41141974

38486735

t

c

        

0.010

0.942

8176188

50

BR1_045505

41141623

38486384

t

g

    

0.063

0.644

    

6416927

51

BR1_0046019

41141109

38485870

g

c

      

0.083

0.208

  

8176198

52

BR1_047826

41139302

38484063

t

a

0.422

0.429

0.362

0.427

0.348

0.114

0.426

0.761

0.479

0.571

8176199

53

BR1_0477839

41139289

38484050

a

c

0.341

0.594

0.258

0.502

0.135

0.167

0.177

0.624

0.396

0.135

4239147

54

BR1_048551

41138577

38483338

t

c

0.440

0.640

0.324

0.677

0.271

0.703

0.394

0.433

0.452

0.711

8176206

55

BR1_050244

41136885

38481646

a

g

    

0.052

0.703

  

0.010

0.942

2236762

56

C_11621042

41135440

38480201

a

t

0.435

0.626

0.358

0.868

0.271

0.703

0.406

0.581

0.479

0.894

1799966

57

C_2615208

41131859

38476620

t

c

0.456

0.456

0.350

0.712

0.233

0.781

0.396

0.359

0.469

0.751

3092987

58

BR1_055669

41131488

38476249

a

g

0.416

0.545

0.350

0.712

0.170

0.510

0.396

0.359

0.458

0.961

8176225

59

BR1_056796

41130361

38475122

g

t

    

0.031

0.823

    

8176232

60

BR1_058369

41128788

38473549

c

t

0.013

0.936

        

8176234

61

BR1_058614

41128545

38473306

a

g

0.437

0.345

0.350

0.712

0.239

0.609

0.396

0.359

0.458

0.961

8176235

62

BR1_058834

41128325

38473086

g

a

0.339

0.872

0.258

0.502

0.167

0.488

0.396

0.359

0.436

0.972

8176236

63

BR1_059589

41127570

38472331

t

c

  

0.008

0.948

0.359

0.556

  

0.010

0.942

8176240

64

BR1_060022

41127137

38471898

t

c

    

0.063

0.644

    

8176242

65

BR1_060520

41126639

38471400

g

a

0.433

0.538

0.350

0.712

0.170

0.510

0.406

0.581

0.458

0.961

8176245

66

BR1_061014

41126145

38470906

t

c

    

0.063

0.644

    

3092994

67

C_2615220

41124590

38469351

c

t

0.434

0.471

0.350

0.712

0.228

0.242

0.396

0.359

0.266

0.808

8176259

68

BR1_062588

41124571

38469332

t

-

    

0.052

0.703

    

8176265

69

BR1_0064398

41122761

38467522

g

a

0.417

0.477

0.350

0.712

0.167

0.729

0.394

0.433

0.260

0.848

2187603

70

BR1_064501

41122658

38467419

g

a

0.422

0.429

0.350

0.712

0.167

0.729

0.396

0.359

0.260

0.848

8176273

71

BR1_066741

41120418

38465179

t

c

0.424

0.580

0.342

0.568

0.167

0.729

0.396

0.359

0.260

0.848

8176278

72

BR1_067978

41119181

38463942

a

g

  

0.008

0.948

0.500

0.564

  

0.021

0.883

8066171

73

BR1_068063

41119096

38463857

g

t

    

0.146

0.237

  

0.010

0.942

NA

74

M_5382insC

41117845

38462606

-

c

0.006

0.957

        

8176289

75

C_2615230

41114821

38459582

t

c

0.441

0.566

0.342

0.568

0.223

0.258

0.396

0.359

0.266

0.808

8176293

76

BR1_073023

41114136

38458897

a

-

      

0.031

0.823

  

4793192

77

BR1_074008

41113155

38457916

a

g

0.435

0.626

0.336

0.794

0.229

0.214

0.396

0.359

0.260

0.848

8176296

78

BR1_074807

41112356

38457117

a

g

0.435

0.703

0.350

0.712

0.229

0.214

0.396

0.359

0.260

0.848

3092988

79

C_2615238

41110467

38455228

c

t

0.424

0.580

0.350

0.712

0.170

0.709

0.396

0.359

0.260

0.848

8176303

80

BR1_076933

41110230

38454991

a

g

    

0.010

0.942

0.042

0.763

  

8176305

81

BR1_077034

41110129

38454890

a

g

0.094

0.753

0.092

0.442

0.021

0.883

  

0.010

0.942

8176307

82

BR1_077328

41109835

38454596

t

c

    

0.063

0.644

    

8068463

83

BR1_079220

41107943

38452704

c

t

    

0.125

0.322

    

8176313

84

BR1_079396

41107767

38452528

g

a

0.006

0.957

0.017

0.896

      

8176316

85

BR1_080570

41106594

38451355

c

a

    

0.021

0.883

    

8176318

86

BR1_081125

41106039

38450800

g

t

0.435

0.963

0.350

0.712

0.167

0.729

0.385

0.491

0.250

1.000

12516

87

BR1_081990

41105173

38449934

c

t

0.435

0.626

0.350

0.712

0.229

0.214

0.406

0.581

0.260

0.848

8176320

88

BR1_082035

41105128

38449889

g

a

0.006

0.957

0.033

0.789

    

0.010

0.942

8176321

89

BR1_082199

41104964

38449725

g

a

    

0.010

0.942

    

8176323

90

BR1_082687

41104476

38449237

c

g

0.429

0.766

0.350

0.712

0.229

0.214

0.396

0.359

0.260

0.848

7223952

91

C_11621012

41103649

38448411

t

c

0.441

0.566

0.356

0.765

0.281

0.569

0.396

0.359

0.287

0.931

9911630

92

C_3178665

41097108

38441868

a

g

0.422

0.429

0.364

0.926

0.266

0.808

0.396

0.359

0.283

0.813

11460963

93

C_2615245

41090062

38435121

-

g

0.441

0.497

0.350

0.712

0.228

0.242

0.396

0.359

0.266

0.808

2298861

94

C_3178699

41085596

38430357

g

a

0.441

0.309

0.350

0.712

0.223

0.258

0.396

0.359

0.266

0.808

2298862

95

C_3178698

41085453

38430214

t

c

0.447

0.383

0.350

0.712

0.208

0.343

0.396

0.359

0.260

0.848

443759

96

C_2287905

41074499

38419260

c

t

0.229

0.129

0.241

0.656

0.354

0.520

0.083

0.208

0.146

0.981

11871636

97

C_11617231

41063582

38408343

a

c

0.235

0.304

0.259

0.386

0.302

0.345

0.167

0.083

0.135

0.278

2271539

98

C_1588447

41059714

38404475

a

g

0.388

0.932

0.388

0.339

0.213

0.447

0.448

0.341

0.277

0.768

690971

99

C_765227

41025330

38370091

g

t

    

0.281

0.885

    

528854

100

C_1588417

41006873

38351634

a

g

0.106

0.230

0.098

0.488

0.479

0.990

  

0.063

0.644

323495

101

C_1588405

40983252

38328013

g

a

0.316

0.182

0.342

0.568

0.208

0.001

0.396

0.135

0.443

0.407

2593595

102

C_3256885

40965010

38309771

a

g

0.124

0.007

0.054

0.672

0.156

0.002

0.135

0.883

0.177

<.0001

324075

103

C_3256881

40935288

38280049

a

g

0.171

0.717

0.195

0.063

0.115

0.370

0.156

0.365

0.330

0.558

2290041

104

C_15883310

40856085

38200846

c

t

0.012

0.913

  

0.302

0.103

0.031

0.823

  

1078523

105

C_2160077

40821525

38166286

a

g

0.480

0.158

0.370

0.650

0.135

0.883

0.478

0.369

0.474

0.075

752313

106

C_1075621

40810589

38155350

t

c

0.363

0.314

0.422

0.851

0.292

0.954

0.406

0.250

0.351

0.251

7359598

107

C_3256867

40806234

38150996

c

t

0.386

0.073

0.440

0.674

0.135

0.883

0.438

0.486

0.383

0.243

2271027

108

C_15959277

40779567

38124328

c

t

    

0.065

0.636

0.031

0.823

  

7214055

109

C_1441435

40761936

38106697

c

g

0.149

0.109

0.008

0.948

0.385

0.003

0.031

0.823

0.021

0.882

9766

110

C_1441436

40761606

38106367

g

a

0.353

0.219

0.433

0.700

0.292

0.954

0.406

0.250

0.344

0.823

1553469

111

C_7529639

40751527

38096288

a

c

0.065

0.248

0.058

0.061

0.031

<.0001

  

0.202

0.943

2271029

112

C_1125369

40744687

38089448

c

a

0.405

0.009

0.350

0.444

0.375

0.441

0.385

0.937

0.402

0.117

3760384

113

C_1441438

40744216

38088977

a

c

0.359

0.020

0.392

0.666

0.447

0.716

0.385

0.937

0.458

0.023

2292749

114

C_1441444

40727349

38072110

c

t

0.217

0.219

0.383

0.518

0.192

0.794

0.375

0.878

0.128

0.316

Number of polymorphic loci

83

 

80

 

99

 

71

 

82

 

Number of SNPs with maf<0.05

11

 

13

 

14

 

6

 

17

 

Mean maf

0.305

 

0.269

 

0.181

 

0.327

 

0.287

 
  1. a April 2003 (Build 33) Position
  2. b March 2006 (Build 36.1) Position
  3. c Com Allele = Common allele
  4. d Min Allele = Minor allele
  5. e maf = Minor allele frequency
  6. f Population private SNPs are shown underlined
  7. gNA= Not Applicable – not in dbSNP