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Table 1 Association of breast cancer risk with 15 SNPs selected from previous GWAS study in the Testing Set.

From: Breast cancer risk assessment with five independent genetic variants and two risk factors in Chinese women

SNP

Chr.

(Cytoband)

Position

Associated genes

GWAS study

Allelesa

Call

Rate

(%)

P b

MAFc

MAFd

Case (%)

Control (%)

P e

rs13387042

2q35

217614077

TNP1, IGFBP5,

IGFBP2

Stacey, 2007 (12)

Thomas, 2009 (13)

G > A

98.65

0.41

0.11

0.12

1.39/25.87/72.74

1.01/21.08/77.91

0.039

rs4973768

3p24.1

27391017

SLC4A7

Ahmed, 2009 (8)

C > T

97.58

0.91

0.17

0.19

3.05/35.05/61.90

3.63/31.52/64.85

0.265

rs2307032

3p24.1

27407999

SLC4A7

Ahmed, 2009 (8)

C > T

97.92

0.08

0.41

0.40

18.58/50.64/30.78

17.61/45.23/37.16

0.017

rs16886165

5p11.2

56058840

MAP3K1

Thomas, 2009 (13)

T > G

96.34

0.65

0.31

0.34

12.10/46.98/40.93

11.49/45.98/42.53

0.781

rs889312

5q11.2

56067641

MAP3K1

Easton, 2007 (9)

C > A

98.31

0.23

0.50

0.48

21.55/50.41/28.04

22.03/52.09/25.88

0.595

rs4415084

5p12

44698272

Unknown

Stacey, 2008 (12)

Thomas,2009 (13)

A > G

96.12

0.03

0.46

0.43

19.95/44.56/35.84

20.41/45.64/33.94

0.798

rs10941679

5p12

44742255

MRPS30

Stacey, 2008 (12)

Thomas,2009 (13)

G > A

97.19

0.95

0.57

0.50

24.23/49.29/26.48

24.83/50.23/24.94

0.768

rs2180341

6q22.33

127642323

ECHDC1, RNF146

Gold, 2008 (10)

A > G

97.30

0.49

0.22

0.26

6.35/43.88/49.76

7.50/37.95/54.55

0.040

rs2046210

6q25.1

151990059

ESR1, C6orf97

Zheng, 2009 (14)

G > A

98.48

0.50

0.35

0.34

18.35/47.97/33.68

12.36/44.16/43.48

1.26 × 10-5

rs13281615

8q24.21

128424800

Unknown

Easton, 2007 (9)

A > G

97.98

0.59

0.57

0.49

23.56/52.40/24.03

24.63/49.04/26.32

0.353

rs1562430

8q24.21

128457034

Unknown

Thomas 2009 (13)

T > C

98.82

0.11

0.20

0.18

2.75/27.38/69.87

2.49/31.33/66.18

0.191

rs2981582

10q26.13

123342307

FGFR2

Easton, 2007 (9)

C > T

99.44

0.94

0.33

0.31

12.61/45.87/41.51

9.82/43.3/46.88

0.037

rs3817198

11p15.5

1865582

LSP1

Easton, 2007 (9)

T > C

98.82

0.88

0.09

0.12

2.41/23.79/73.79

1.58/21.53/76.89

0.213

rs12443621

16q12.1

51105538

TNRC9

Easton, 2007 (9)

G > A

99.10

0.34

0.39

0.45

18.23/48.17/33.60

19.10/51.12/29.78

0.227

rs6504950

17q23.2

50411470

COX11

Ahmed, 2009 (8)

G > A

98.71

0.84

0.10

0.09

0.35/14.14/85.52

0.78/15.92/83.30

0.264

  1. a Major > Minor; b P-values for Hardy-Weinberg equilibrium(HWE) in the controls by exact test; c Minor Allele Frequency (MAF) of Chinese Han population from Beijing (CHB) based on the International HapMap project (Phase II+III, rel 27); d Minor Allele Frequency (MAF) in controls; e P-values for genotypic frequency between cases and controls by Fisher's exact test.
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Breast Cancer Research

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