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Table 1 Association of previously identified loci with breast cancer risk in 2,257 cases and 2,052 controls in the Seoul Breast Cancer Study

From: A genome-wide association study identifies a breast cancer risk variant in ERBB4 at 2q34: results from the Seoul Breast Cancer Study

Region/Reported gene(s)

SNP

Loci evaluated in this study

Loci reported in genome-wide association studies

  

Risk allele

RAF

OR (95% CI)a

P

Genotyping

Risk allele

RAF

OR (95% CI)

P

Reference

1p11.2/NOTCH2, FCGR1B

rs11249433

C

0.04

1.11 (0.88-1.40)

3.8 × 10-1

Imputed

C

0.39

1.16 (1.09-1.24)

7 × 10-10

[8]

2q35/Intergenic

rs13387042

A

0.10

1.11 (0.96-1.28)

1.6 × 10-1

Imputed

A

0.50

1.2 (1.14-1.26)

1 × 10-13

[6]

3p24.1/SLC4A7

rs4973768

T

0.22

1.09 (0.98-1.21)

1.2 × 10-1

Imputed

T

0.47

1.16 (1.10-1.24)

6 × 10-7

[9]

5q11.2/MAP3K1

rs16886165

G

0.35

1.14 (1.04-1.25)

6.5 × 10-3

Imputed

G

0.15

1.23 (1.12-1.35)

5 × 10-7

[8]

 

rs889312

C

0.55

1.16 (1.06-1.27)

8.5 × 10-4

Imputed

C

0.28

1.13 (1.10-1.16)

7 × 10-20

[5]

5p12/MRPS30

rs7716600

A

0.48

1.13 (1.03-1.23)

6.9 × 10-3

Imputed

A

0.23

1.24 (1.14-1.34)

7 × 10-7

[34]

 

rs4415084

T

0.56

1.09 (0.99-1.19)

7.8 × 10-2

Imputed

T

0.42

1.17 (1.11-1.22)

8 × 10-11

[24]

5p15.2/ROPN1L

rs1092913

G

0.30

1.11 (1.01-1.22)

2.8 × 10-2

Imputed

T

0.13

1.45 (1.24-1.69)

2 × 10-6

[35]

6q22.33/ECHDC1, RNF146

rs2180341

G

0.27

1.03 (0.93-1.13)

6.0 × 10-1

Typed

G

0.21

1.41 (1.25-1.59)

3 × 10-8

[36]

6q25.1/ESR1, C6orf97

rs3734805

C

0.33

1.20 (1.09-1.33)

1.8 × 10-4

Imputed

C

0.08

1.19 (1.11-1.27)

1 × 10-7

[24]

 

rs2046210

A

0.35

1.29 (1.18-1.41)

5.8 × 10-8

Typed

A

0.37

1.29 (1.21-1.37)

2 × 10-15

[10]

7q32.3/NR

rs2048672

C

0.49

1.05 (0.97-1.15)

2.3 × 10-1

Typed

C

0.45

1.11 (1.05-1.17)

6 × 10-6

[12]

8q24.21/Intergenic

rs13281615

C

0.57

1.04 (0.95-1.14)

3.8 × 10-1

Imputed

C

0.40

1.08 (1.05-1.11)

5 × 10-12

[5]

 

rs1562430

T

0.87

1.16 (1.01-1.33)

3.0 × 10-2

Imputed

T

0.58

1.17 (1.10-1.25)

6 × 10-7

[9]

9p21.3/CDKN2A, CDKN2B

rs1011970

T

0.07

1.00 (0.84-1.19)

9.9 × 10-1

Imputed

T

0.17

1.09 (1.04-1.14)

3 × 10-8

[9]

9q31.2/KLF4, RAD23B, ACTL7A

rs865686

T

0.93

1.02 (0.86-1.21)

8.1 × 10-1

Imputed

T

0.61

1.12 (1.09-1.18)

2 × 10-10

[24]

10p15.1/ANKRD16, FBXO18

rs2380205

C

0.91

1.11 (0.95-1.29)

1.8 × 10-1

Typed

C

0.57

1.06 (1.02-1.10)

5 × 10-7

[9]

10q21.2/ZNF365

rs10995190

G

0.98

1.02 (0.76-1.38)

8.9 × 10-1

Imputed

G

0.85

1.16 (1.10-1.22)

5 × 10-15

[9]

 

rs10822013

T

0.47

1.06 (0.97-1.15)

2.1 × 10-1

Typed

T

0.47

1.12 (1.06-1.18)

6 × 10-9

[12]

10q22.3/ZMIZ1

rs704010

A

0.29

1.08 (0.98-1.19)

1.2 × 10-1

Typed

A

0.39

1.07 (1.03-1.11)

4 × 10-9

[9]

10q26.13/FGFR2

rs10510102

G

0.18

1.01 (0.90-1.13)

8.4 × 10-1

Typed

G

0.17

1.12 (1.07-1.17)

2 × 10-6

[24]

 

rs10736303b

G

0.53

1.17 (1.07-1.28)

4.4 × 10-4

Typed

T

0.41

1.17 (1.07-1.27)

2 × 10-10

[8]

11p15.5/LSP1

rs3817198

C

0.16

1.00 (0.89-1.13)

9.5 × 10-1

Typed

C

0.30

1.07 (1.04-1.11)

3 × 10-9

[5]

14q24.1/RAD51L1

rs10483813c

T

0.97

1.21 (0.93-1.56)

1.6 × 10-1

Imputed

C

0.76

1.06 (1.01-1.14)

2 × 10-7

[8]

16q12.1/TOX3

rs4784227

T

0.29

1.27 (1.15-1.40)

1.5 × 10-6

Typed

T

0.24

1.24 (1.20-1.29)

1 × 10-28

[11]

 

rs3803662

T

0.64

1.24 (1.14-1.36)

2.4 × 10-6

Typed

T

0.27

1.28 (1.21-1.35)

6 × 10-19

[5]

19q13.41/ZNF577

rs10411161

C

0.72

1.01 (0.92-1.11)

8.6 × 10-1

Typed

T

0.13

1.42 (1.22-1.65)

7 × 10-6

[35]

  1. The average call rate was 99.8% (range of 99.4% to 100%) for typed single-nucleotide polymorphisms (SNPs), and the average of imputation quality score from MACH (r2) was 0.97 (range of 0.95 to 1.00). aPer-allele odds ratio (OR) adjusted for age; bproxy SNP of rs2981579 (r2 = 0.48 in CHB+JPT; r2 = 0.74 in CEU); cproxy SNP of rs999737 (r2 = 0.50 in CHB+JPT; r2 = 0.98 in CEU). CEU, CEPH Utah residents with ancestry from Northern and Western Europe; CHB+JPT, Han Chinese from Beijing + Japanese from Tokyo; CI, confidence interval; RAF, risk allele frequency.