Table 6 List of most significant SNPs in the CCV analysis for BRCA2 mutation carriers.

From: A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Fine mapping regiona

Signalb

#CCVc

Location

SNP named

Chre

Positionf

Nearest gene

Localisation

Estimated effect allele

Referent allele

Frequency g

r² h

Pi

ORj

PCIMBAk

HRCIMBAl

chr2:67099466-68099466

1

78

2p14

rs12470785

2

67634003

ETAA1

Intronic

G

A

0.30

0.98

4.20e−11

0.85

7.70e−05

0.89

chr13:31015494-32515494

1

8

13q13.1

rs79183898

13

32221794

B3GALTL, RXFP2

Intergenic

A

T

0.07

0.84

1.10e−10

1.33

3.60e−01

1.04

2

23

13q12.3

rs71434801

13

31249461

USPL1, ALOX5AP

Intergenic

G

C

0.13

0.76

3.40e−08

1.22

8.40e−01

0.99

3

35

13q12.3

rs77197167

13

31693513

WDR95P, HSPH1

Intergenic

C

T

0.09

0.76

1.80e−07

1.25

4.00e−01

1.04

4

7

13q12.3

rs114300732

13

31662987

WDR95P

Intronic

T

C

0.07

0.90

1.70e−08

0.67

8.80e−02

1.09

5

12

13q13.1

13:32231513:CAA:C

13

32231513

B3GALTL, RXFP2

Intergenic

CAA

C

0.25

0.92

8.40e−07

0.86

1.70e−02

1.08

6

6

13q13.1

rs1623189

13

32232683

B3GALTL, RXFP2

Intergenic

G

T

0.26

0.95

1.30e−31

2.70

6.60e−01

1.01

chr13:33395975-34395975

1

1

13q13.1

rs736596

13

33776506

STARD13

Intronic

T

G

0.09

0.66

1.20e−12

1.37

2.50e−01

0.95

2

1

13q13.1

rs77889880

13

33776161

STARD13

Intronic

T

A

0.10

0.80

3.00e−21

0.51

1.90e−02

1.12

3

1

13q13.1

rs67776313

13

33934343

RP11-141M1.3

Intronic

A

AT

0.33

0.70

7.70e−12

0.81

4.60e−01

0.98

4

42

13q13.1

rs71196514

13

33800572

STARD13

Intronic

C

CT

0.38

0.67

1.00e−07

0.86

6.20e−01

1.01

5

52

13q13.1

rs2555605

13

33833810

STARD13

Intronic

C

T

0.36

1.00

4.60e−08

0.87

2.00e−01

1.03

6

46

13q13.1

rs74796280

13

33700860

STARD13

Intronic

C

A

0.06

0.96

4.70e−07

0.77

3.10e−02

0.89

chr13:34793902-35793902

1

18

13q13.2

rs4943263

13

35376357

RP11-266E6.3, RP11-307O13.1

intergenic

T

C

0.27

0.99

6.30e−11

1.18

9.80e−01

1.00

2

3

13q13.2

rs2202781

13

35292372

RP11-266E6.3, RP11-307O13.1

Intergenic

G

A

0.24

0.93

3.10e−11

1.20

6.00e−01

0.98

3

40

13q13.2

rs55675572

13

35315594

RP11-266E6.3, RP11-307O13.1

intergenic

A

T

0.40

0.77

5.60e−08

0.86

7.50e−01

0.99

4

21

13q13.2

rs17755120

13

35270340

RP11-266E6.3, RP11-307O13.1

intergenic

T

A

0.20

0.98

6.30e−07

0.76

4.80e−01

0.98

  1. N = 62,822 breast cancer cases (57,725 BCAC cases and 5,097 BRCA2 mutation carrier cases).
  2. aSignificant region in the main analysis used to look for credible causal variants (CCV).
  3. bSignal number (the first one corresponds to the CCV set without any adjustment and the following are those with adjustment on each most significant SNP of the previous signals).
  4. cNumber of credible causal variants at each signal (SNP with p-value at 2 order of magnitude of the most significant one).
  5. dThe most significant SNP after adjustment on the most significant SNPs of the previous signals (except for these of the signal 1).
  6. eChromosome.
  7. fBuild 37 position.
  8. gFrequency of the allele for which effect is estimated in BCAC cases (OncoArray dataset).
  9. hImputation accuracy.
  10. ip-value in the case-only analysis after adjustment on the most significant SNPs of the previous signals (except for these of the signal 1).
  11. jPer allele odds ratio estimated in the case-only analysis. OR values were computed from a two sided logistic regression using a 1df lrtest adjusted for age at BC diagnosis, country, the first four principal components and the most significant SNPs of the previous signals (except for these of the signal 1).
  12. kp-value found in CIMBA cohort analysis.
  13. lPer allele hazard ratio estimated in CIMBA cohort analysis.
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