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Table 3 Independent association signals in the meta-analysis of BCAC (ER-) and BRCA1 mutation carriers from CIMBA

From: Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

 

SNPs

Position (hg 19)

Alleles

EAF

LD (r 2)§

Univariate analysis

Conditional analysis

Per-allele effect (95 % CI)a

P-trend

Per-allele effect (95 % CI)b

P-trend

Indexǂ

rs10771399

28155080

G*/A

0.10

-

0.86 (0.80–0.91)

3 × 10-6

-

-

Meta-analysis of ER-negative cancer (BCAC + CIMBA)

      

BCAC ER-

        

 Signal 1

rs7297051

28174817

T*/C

0.24

0.42

0.87 (0.83–0.91)

3 × 10-10

0.89 (0.85–0.94)

1 × 10-5

 Signal 4

rs113824616

28184905

C*/T

0.05

0.40

0.75 (0.67–0.84)

5 × 10-7

0.86 (0.76–0.98)

0.02

CIMBA BRCA1 mutation carriers

 Signal 1

rs7297051

28174817

T*/C

0.23

0.37

0.89 (0.85–0.93)

3 × 10-7

0.94 (0.90–0.98)

0.003

 Signal 4

rs113824616

28184905

C*/T

0.04

0.49

0.73 (0.64–0.82)

1 × 10-7

0.83 (0.74–0.93)

0.001

  1. Effect for Breast Cancer Association Consortium (BCAC): odds ratio; effect for Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) cohort: hazard ratio. *Effect alleles. aAdjusted for studies, and the top principal components. bIncluded both variants, and adjusted for studies and the top principal components. SNPs single nucleotide polymorphisms, EAF effect allele frequency in the or (BCAC) controls, LD linkage disequilibrium, CI confidence interval, ER estrogen receptor. §represents LD with the index SNP rs10771399. ǂrepresented the index SNP, Identified in the initial genome-wide association study conducted in women of European descent [1]