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Table 1 Allele distributions of SNPs in TF pathway genes in cases and controls

From: Increased coagulation activity and genetic polymorphisms in the F5, F10 and EPCRgenes are associated with breast cancer: a case-control study

Gene

Chr

SNP

Bp (hg18)

Region

Minor allele

Major allele

Freqency cases

Frequency controls

χ2

OR

P-value (unadj.)

FDR

F2

11

rs2070852

46701501

Intronic

C

G

0.290

0.316

0.99

0.89

0.319

0.83

F2

11

rs3136516

46717332

Intronic

G

A

0.448

0.448

0.00

1.00

0.996

1.00

F2

11

rs5896

46701579

Coding (T > M)

T

C

0.133

0.127

0.09

1.05

0.760

0.93

F2

11

rs1799963

46717631

3UTR

A

G

0.013

0.005

2.20

2.60

0.138

0.61

F3

1

rs3917643

94774455

Intronic

C

T

0.058

0.080

2.58

0.70

0.109

0.57

F3

1

rs696619

94777808

Intronic

A

G

0.414

0.440

0.87

0.90

0.351

0.83

F3

1

rs1324214

94769876

Intronic

A

G

0.240

0.271

1.59

0.85

0.207

0.70

F3

1

rs3917615

94774578

Intronic

T

C

0.439

0.433

0.04

1.02

0.839

0.93

F5

1

rs12120605

167789178

Intronic

T*

G

0.140

0.100

4.93

1.47

0.026

0.22

F5

1

rs6427202

167795454

Intronic

C*

T

0.454

0.394

4.82

1.28

0.028

0.22

F5

1

rs9332542

167805907

Intronic

A

G*

0.286

0.344

5.16

0.76

0.023

0.22

F5

1

rs6427199

167790161

Intronic

A

G*

0.364

0.420

4.36

0.79

0.037

0.23

F5

1

rs6012

167795204

Intronic

T

C

0.162

0.164

0.01

0.98

0.906

0.93

F5

1

rs4524

167778379

Coding (K > R)

C

T

0.261

0.257

0.03

1.02

0.871

0.93

F5

1

rs4656687

167771782

Intronic

C

T

0.323

0.312

0.17

1.05

0.676

0.93

F5

1

rs6025

167785673

Coding (Q > R)

T

C

0.033

0.034

0.02

0.96

0.900

0.93

F5

1

rs9287095

167805090

Intronic

A

G

0.094

0.104

0.34

0.90

0.561

0.93

F5

1

rs10158595

167786988

Intronic

T

C

0.223

0.248

1.14

0.87

0.286

0.83

F5

1

rs9332618

167767105

Intronic

A

G

0.133

0.139

0.08

0.95

0.773

0.93

F7

13

rs491098

112817347

Intronic

C

G

0.106

0.117

0.39

0.90

0.530

0.93

F10

13

rs3093261

112824083

Near 5UTR

T*

C

0.460

0.391

6.41

1.33

0.011

0.22

F10

13

rs3211744

112832999

Intronic

T

G

0.136

0.154

0.85

0.87

0.358

0.83

F10

13

rs2026160

112840894

Intronic

C

A

0.284

0.258

1.08

1.14

0.298

0.83

F10

13

rs9549675

112846885

Intronic

T

C

0.205

0.239

2.10

0.83

0.148

0.61

F10

13

rs3211719

112825510

Intronic

G

A

0.252

0.245

0.09

1.04

0.769

0.93

F10

13

rs3211752

112835460

Intronic

G

A

0.499

0.489

0.13

1.04

0.716

0.93

F10

13

rs556694

112828042

Intronic

C

T

0.093

0.089

0.04

1.04

0.836

0.93

F10

13

rs3211770

112841850

Intronic

A

G

0.109

0.113

0.05

0.96

0.818

0.93

F10

13

rs473598

112849190

Intronic

A

G

0.128

0.137

0.23

0.92

0.629

0.93

EPCR

20

rs2069948

33226150

Intronic

C*

T

0.468

0.408

4.72

1.27

0.030

0.22

TFPI

2

rs2192825

188099064

Intronic

C

T

0.439

0.402

1.81

1.16

0.178

0.66

TFPI

2

rs7594359

188117093

Intronic

T

C

0.461

0.441

0.52

1.08

0.472

0.93

TFPI

2

rs2192824

188077036

Intronic

T

C

0.449

0.428

0.54

1.09

0.461

0.93

TFPI

2

rs13424790

188032097

Downstream

G

T

0.317

0.310

0.08

1.03

0.778

0.93

TFPI

2

rs8176548

188048580

Intronic

T

C

0.351

0.347

0.02

1.02

0.878

0.93

TFPI

2

rs10187622

188122406

Intronic

T

C

0.161

0.165

0.03

0.97

0.864

0.93

TFPI

2

rs12613071

188096556

Intronic

C

T

0.202

0.195

0.09

1.04

0.762

0.93

  1. P-values were determined by the χ2 -test. Alleles for the positive DNA strand (UCSC annotated) are shown. Significantly associated SNPs; bold, and factor V Leiden (F5 rs6025) and prothrombin G20210A (F2 rs1799963); italic. *Risk alleles for significant SNPs.
  2. Chr: chromosome. OR: Odds ratio as determined for the minor allele with the major allele as reference. FDR: False discovery rate as described by Benjamini and Hochberg [28].