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Table 3 Genes significantly associated with estrogen receptor (ER)-positive and/or ER-negative breast cancer after conditioning on nearby GWAS SNPs for breast cancer risk

From: Expression- and splicing-based multi-tissue transcriptome-wide association studies identified multiple genes for breast cancer by estrogen-receptor status

Loci

Gene Name

Closest GWAS Index SNP

Distance to Closest GWAS Index SNP (kb)

Min. 11 Tissue ACAT COJO p-valuea

Min. Breast COJO p-valueb

COJO TWAS-significant Approachesc

Estrogen receptor positive

1q21.1, L1

FCGR1CP

rs1552172

1846.8

3.33E-11

NA

splice

1q21.1, L1

FAM72C

rs1552172

1758.3

1.25E-11

NA

express

1q21.1, L2

ITGA10

rs143384623

60.4

1.20E-06

1.58E-06

splice

2q35

DIRC3

rs6436017

102.1

2.29E-10

1.74E-01

express

3p24.1, L1

NEK10

rs4973768

5.1

1.82E-11

2.02E-12

express

5p12

MRPS30

rs930395

1.9

2.78E-16

2.78E-16

express|splice

5p12

RP11-53O19.3

rs930395

3.7

5.55E-17

9.11E-01

express

8q21.13

HNF4G

rs72658071

14.4

1.47E-10

NA

express|splice

10p12.31-p12.2

PIP4K2A

rs541079479

0

5.22E-07

6.12E-07

splice

11p15.5, L2

LSP1

rs576603

0.6

9.57E-13

2.82E-04

express

11p15.5, L2

TNNT3

rs576603

26.8

5.22E-12

5.12E-04

express|splice

11q13.3

RP11-554A11.8

rs72932540

0

3.44E-07

NA

express

12p11.22, L1

CCDC91

rs7297051

111.4

6.45E-08

5.34E-08

express|splice

14q32.11-q32.12

CCDC88C

rs150658557

4.7

8.74E-07

1.35E-07

splice

16q12.1-q12.2

TOX3

rs3803662

4.6

< 5.50E-17

2.21E-02

express

17q22

COX11

rs6504950

10.4

2.32E-08

2.97E-01

splice

18q11.2, L2

CHST9

rs232320

0

8.27E-07

NA

splice

19p13.11, L2

LRRC25

rs7258465

25.2

1.15E-09

2.19E-01

express

19p13.11, L2

SSBP4

rs7258465

0

6.34E-09

3.89E-08

splice

19p13.11, L2

ISYNA1

rs7258465

11.6

6.01E-08

3.00E-08

express

19q13.32

GIPR

rs61373376

0

1.40E-06

1.55E-02

express

22q12.1-q12.2

TTC28

rs62235681

4.9

9.72E-10

6.49E-02

express

22q12.1-q12.2

CHEK2

rs62235681

3

1.16E-12

6.57E-02

express|splice

22q12.1-q12.2

HSCB

rs17879961

16.9

2.02E-12

8.42E-08

express|splice

22q12.1-q12.2

CCDC117

rs17879961

47.6

1.46E-09

1.17E-06

express|splice

22q12.1-q12.2

XBP1

rs17879961

69.5

7.97E-09

5.37E-06

express

22q12.1-q12.2

CTA-292E10.6

rs4822992

24.2

2.91E-09

6.63E-04

splice

Estrogen receptor negative

1q32.1, L4

MDM4

rs4245739

0

3.29E-09

9.86E-10

splice

2q14.2

RALB

rs4528762

27.2

4.52E-07

1.69E-07

splice

2q14.2

INHBB

rs11903787

15.5

6.09E-07

2.66E-01

express

2q33.1

FAM126B

rs13015648

54.1

5.23E-07

8.21E-03

express

2q33.1

NDUFB3

rs13015648

40.1

3.47E-08

NA

express

2q33.1

CFLAR

rs13015648

0

5.34E-06

3.40E-06

express

11q22.3

ACAT1

rs199504893

249.1

2.18E-07

4.45E-08

splice

12p11.22, L1

CCDC91

rs7297051

111.4

2.71E-07

2.32E-07

splice

16q12.1-q12.2

TOX3

rs3803662

4.6

1.38E-10

6.51E-01

express

  1. Abbreviations:
  2. TWAS, transcriptome-wide association study; ER+, estrogen receptor-positive; ER-, estrogen receptor-negative; ER+, estrogen receptor-positive; COJO, conditional & joint association analysis using GWAS summary statistics.
  3. a The minimum joint-tissue TWAS p-value conditioned on GWAS index SNPs between either the expression-based or splicing-based approach.
  4. b The minimum TWAS p-value in breast tissue conditioned on GWAS index SNPs between either the expression-based approach or splicing-based approach.
  5. c “Express” indicates the listed gene was identified using only the expression-based TWAS approach in either only breast tissue or jointly across all tissues after conditioning on nearby GWAS index SNPs. “splice” indicates the listed gene was identified using only the splicing-based TWAS approach in either only breast tissue or jointly across all tissues after conditioning on nearby GWAS index SNPs. “express|splice” indicates the listed gene was identified in either expression-based or splicing-based approaches in either breast tissue or jointly across all tissues after conditioning on nearby GWAS index SNPs.
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Breast Cancer Research

ISSN: 1465-542X

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