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Table 2 Most significant SNPs in 33 genomic regions associating at the p < 10−6 level with sporadic, BRCA-mutation-negative breast cancer cases in the Sardinian population

From: Genome-wide association study of susceptibility loci for breast cancer in Sardinian population

Chromosomal region

SNP

Position

Alleles

Frequency

RSQR

OR (CI 95%)

p

Gene

Cases

Controls

1p35.1

rs9425977

34238042

C/T

0.082

0.059

0.379

2.597 (1.817 - 3.709)

9.51E-08

CSMD2

1p34.1

rs2477618

44271050

C/G

0.077

0.058

0.416

2.312 (1.647 -3.245)

9.13E-07

-

1p13.3

rs345299

108249656

A/C

0.465

0.534

0.957

0.755 (0.676 - 0.845)

9.40E-07

VAV3

1q32.1

rs6661074

203605742

A/G

0.483

0.425

0.731

1.408 (1.235 - 1.605)

3.10E-07

LEMD1

2p25.3

rs13393791

3239073

C/T

0.074

0.039

0.989

1.862 (1.469 - 2.361)

1.99E-07

TSSC1

2p21

rs17032957

45134208

A/G

0.701

0.747

0.462

0.597 (0.500 - 0.712)

9.17E-09

SIX2/SIX3

2q37.1

rs838436

232291757

A/G

0.908

0.926

0.308

0.415 (0.291 - 0.592)

8.45E-07

-

3p14.1

rs9810816

67158548

C/G

0.935

0.955

0.404

0.368 (0.251 - 0.541)

1.86E-07

-

5q35.2

rs17076993

173564400

C/T

0.071

0.049

0.447

2.507 (1.768 - 3.553)

1.29E-07

-

6q23.1

rs3777428

130495535

C/T

0.926

0.952

0.720

0.509 (0.387 - 0.668)

8.48E-07

L3MBTL3

7p14.2

rs6968002

36531229

C/T

0.938

0.958

0.533

0.431 (0.308 - 0.603)

6.32E-07

AOAH

8q24.3

rs11785598

144537061

C/T

0.948

0.929

0.328

3.420 (2.223 - 5.266)

6.40E-09

RHPN1

9q22.32

rs10512243

97815280

A/G

0.093

0.056

0.913

1.754 (1.411 - 2.181)

2.78E-07

-

9q31.2

rs10979327

110160516

G/T

0.112

0.060

0.632

3.851 (2.955 - 5.016)

2.92E-25

-

9q33.3

rs1928482

125472269

C/T

0.361

0.303

0.978

1.362 (1.206 - 1.538)

4.87E-07

DENND1A

9q34.13

rs1633769

134869098

C/G

0.769

0.803

0.393

0.558 (0.452 - 0.690)

6.07E-08

-

9q34.3

rs3811159

136828478

A/G

0.608

0.661

0.683

0.706 (0.616 - 0.810)

6.07E-07

COL5A1

10q21.1

rs1903974

53549083

A/G

0.047

0.077

0.865

0.527 (0.409 - 0.680)

4.38E-07

PRKG1

11p12

rs7947387

38902742

A/G

0.050

0.069

0.333

0.347 (0.230 - 0.523)

2.45E-07

-

12q21.1

rs11178748

70021794

A/G

0.100

0.078

0.897

1.673 (1.366 - 2.046)

5.15E-07

TSPAN8

12q23.3

rs7488485

105789959

C/T

0.097

0.073

0.404

2.348 (1.722 - 3.198)

3.17E-08

RIC8B

13q21.1

rs9569528

56234110

C/T

0.074

0.051

0.492

2.481 (1.782 - 3.456)

5.27E-08

-

14q23.1

rs17097373

59896563

C/T

0.076

0.058

0.770

1.861 (1.448 - 2.391)

9.43E-07

-

15q12

rs17651375

25763160

C/T

0.084

0.056

0.934

1.761 (1.417 - 2.189)

2.93E-07

OCA2

16q12.1

rs2193094

51123955

G/T

0.557

0.478

0.982

1.337 (1.198 - 1.491)

1.70E-07

TOX3

16q21

rs8045513

60720397

A/T

0.059

0.088

0.606

0.430 (0.326 - 0.569)

9.49E-10

-

18p11.22

rs17436811

10080771

C/T

0.084

0.058

0.644

2.002 (1.536 - 2.608)

2.20E-07

-

19q13.31

rs17725531

49018018

G/T

0.140

0.099

0.930

1.560 (1.311 - 1.858)

5.82E-07

-

20p12.2

rs6039942

10376146

A/G

0.100

0.068

0.623

2.005 (1.565 - 2.565)

2.13E-08

C20orf94

21q22.11

rs2833424

31774071

A/G

0.293

0.239

0.985

1.365 (1.206 - 1.544)

8.42E-07

TIAM1

21q22.11

rs963950

33438577

C/T

0.930

0.883

0.986

1.742 (1.432 - 2.119)

1.24E-08

IFNAR2

21q22.13

rs857989

38042001

C/G

0.154

0.111

0.896

1.537 (1.301 - 1.816)

3.72E-07

KCNJ6

22q12.3

rs6000351

35340813

A/G

0.093

0.069

0.445

2.100 (1.556 - 2.835)

7.44E-07

CACNG2

  1. The table reports, for each SNP, the genomic cytoband, the rs name, the position in build36, the corresponding alleles, the frequency in cases and controls, the imputation quality, the OR and its confidence interval, the pvalue and the most candidate gene within 200 kb. Additional SNPs in the same genomic regions are listed in Additional file 3: Table S2.