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Table 2 The rare allele frequencies of 51 single nucleotide polymorphisms (SNPs) in breast cancer patients and control subjects and their association with risk of breast cancer, The Singapore Chinese Health Study, 1993 to 1998

From: Breast cancer risk assessment using genetic variants and risk factors in a Singapore Chinese population

Chr

Genes in or near region

SNP

Effect allele

RAF in controls

RAF in cases

Per-allele OR (95% CI)

SE

Pvalue*

Pooled OR

FDR-correctedPhet

1

PEX14

rs616488

G

0.348

0.361

1.06 (0.89, 1.26)

0.09

0.510

0.94

0.790

1

PTPN22/BCL2L15/AP4B1/DCLRE1B/HIPK1

rs11552449

A

0.596

0.556

0.85 (0.72, 0.99)

0.08

0.040

1.06

0.068

1

FCGR1B

rs11249433

G

0.029

0.026

0.85 (0.52, 1.39)

0.25

0.517

1.09

0.371

2

INHBB-

rs4849887

A

0.259

0.269

1.05 (0.87, 1.25)

0.09

0.634

0.92

0.561

2

METAP1D/DLX1/DLX2

rs2016394

A

0.195

0.191

0.96 (0.79, 1.18)

0.10

0.727

0.95

0.790

2

TNP1‡

rs13387042

G

0.907

0.883

0.77 (0.60, 0.99)

0.13

0.045

0.93

0.062

2

DIRC3

rs16857609

C

0.376

0.367

1.07 (0.90, 1.27)

0.09

0.462

1.08

0.977

3

ITPR1/EGOT

rs6762644

G

0.098

0.096

0.97 (0.73, 1.29)

0.14

0.841

1.07

0.790

3

SLC4A7

rs4973768

A

0.190

0.186

0.97 (0.80, 1.18)

0.10

0.757

1.11

0.473

3

TGFBR2

rs12493607

G

0.278

0.262

0.91 (0.76, 1.09)

0.09

0.290

1.06

0.619

4

TET2

rs9790517

A

0.613

0.635

1.09 (0.93, 1.29)

0.08

0.293

1.05

0.440

4

ADAM29

rs6828523

A

0.275

0.271

0.99 (0.82, 1.18)

0.09

0.879

0.90

0.729

5

5p12 (intergenic)

rs4415084

C

0.441

0.434

0.96 (0.82, 1.14)

0.08

0.668

1.15

0.087

5

MRPS30

rs10941679

G

0.499

0.519

1.09 (0.93, 1.29)

0.08

0.289

1.12

0.409

5

MAP3K1‡

rs889312

C

0.589

0.577

0.96 (0.82, 1.14)

0.08

0.666

1.05

0.727

5

RAB3C

rs10472076

G

0.247

0.260

1.07 (0.89, 1.28)

0.09

0.465

1.04

0.500

5

EBF1

rs1432679

G

0.631

0.642

1.05 (0.89, 1.24)

0.08

0.558

1.07

0.931

6

FOXQ1†

rs11242675

A

0.597

0.633

1.15 (0.98, 1.35)

0.08

0.088

-

-

6

ECHDC1/RNF146

rs2180341

G

0.181

0.198

1.09 (0.90, 1.33)

0.10

0.365

1.31

0.100

6

RANBP9

rs204247

G

0.588

0.611

1.10 (0.94, 1.29)

0.08

0.248

1.05

0.911

6

FAM46A

rs17529111

G

0.218

0.206

0.92 (0.75, 1.12)

0.10

0.404

1.06

0.675

6

ESR1

rs3757318

A

0.276

0.316

1.20 (1.01, 1.42)

0.09

0.039

1.04

0.790

6

ESR1‡

rs2046210

A

0.380

0.434

1.25 (1.06, 1.46)

0.08

0.008

1.27

0.970

7

ARHGEF5

rs720475

A

0.046

0.041

0.90 (0.61, 1.33)

0.20

0.596

0.94

0.941

8

RPL17P33

rs9693444

A

0.282

0.288

1.04 (0.87, 1.24)

0.09

0.691

1.07

0.977

8

8q24

rs13281615

G

0.502

0.500

0.99 (0.84, 1.16)

0.08

0.872

1.07

0.215

8

8q24

rs1562430

C

0.181

0.184

1.03 (0.83, 1.27)

0.11

0.820

0.87

0.273

9

CDKN2A

rs1011970

A

0.096

0.095

0.98 (0.75, 1.28)

0.14

0.875

1.07

0.639

9

KLF4

rs10759243

A

0.431

0.476

1.20 (1.02, 1.41)

0.08

0.027

1.06

0.790

9

KLF4

rs865686

C

0.057

0.067

1.19 (0.87, 1.64)

0.16

0.275

0.90

0.150

10

ZNF365

rs10822013

T

0.500

0.517

1.07 (0.91, 1.25)

0.08

0.409

1.08

0.387

10

ZNF365‡

rs10995190

A

0.012

0.013

1.14 (0.57, 2.30)

0.36

0.713

1.06

0.350

10

ZMIZ1

rs704010

A

0.369

0.397

1.12 (0.95, 1.33)

0.08

0.169

1.08

0.473

10

FGFR2‡

rs1219648

G

0.404

0.427

1.08 (0.92, 1.27)

0.08

0.343

1.14

0.560

10

FGFR2

rs2981582

A

0.338

0.370

1.14 (0.96, 1.34)

0.08

0.128

1.26

0.451

11

LSP1

rs3817198

G

0.095

0.108

1.14 (0.89, 1.46)

0.13

0.311

1.07

0.931

11

DKFZp761E198/OVOL1/SNX32/CFL1

rs3903072

A

0.210

0.175

0.81 (0.66, 0.99)

0.10

0.039

0.95

0.268

11

BARX2

rs11820646

A

0.489

0.509

1.09 (0.93, 1.28)

0.08

0.278

0.95

0.574

12

ATF7IP

rs12422552

C

0.273

0.325

1.29 (1.08, 1.53)

0.09

0.004

1.06

0.128

12

PTHLH

rs10771399

G

0.192

0.173

0.88 (0.71, 1.08)

0.11

0.221

0.86

0.729

12

NTN4

rs17356907

G

0.253

0.247

0.98 (0.82, 1.18)

0.09

0.839

0.91

0.604

14

PAX9/SLC25A21

rs2236007

A

0.297

0.255

0.83 (0.69, 0.98)

0.09

0.031

0.92

0.469

14

CCDC88C

rs941764

G

0.126

0.140

1.13 (0.90, 1.42)

0.12

0.308

1.06

0.931

16

TOX3

rs4784227

T

0.245

0.274

1.17 (0.97, 1.41)

0.09

0.098

1.23

0.574

16

TOX3

rs3112612

G

0.228

0.210

0.90 (0.74, 1.10)

0.10

0.300

1.13

0.066

16

CDYL2

rs13329835

G

0.053

0.054

1.02 (0.70, 1.46)

0.18

0.938

1.09

0.351

16

MIR1972-2/FTO

rs17817449

C

0.140

0.118

0.83 (0.66, 1.06)

0.12

0.134

0.93

0.079

18

AQP4‡

rs527616

G

0.267

0.266

0.99 (0.83, 1.19)

0.09

0.951

0.98

0.805

18

CHST9

rs1436904

C

0.486

0.509

1.09 (0.93, 1.28)

0.08

0.287

0.96

0.225

19

C19orf61:KCNN4:LYPD5:ZNF283

rs3760982

A

0.136

0.148

1.10 (0.87, 1.38)

0.12

0.437

1.06

0.994

21

NRIP1

rs2823093

A

0.035

0.032

0.90 (0.57, 1.40)

0.23

0.631

0.92

0.994

  1. †A pooled odds ratio (pOR) was not obtained for rs11242675 due to significant heterogeneity with other published studies; ‡a pOR with the Asian studies was obtained due to heterogeneity with the results of European studies.*P value was derived from conditional logistic regression analysis. Chr, chromosome; RAF, risk allele frequency; FDR, false discovery rate.