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Table 1 Independent association signals identified for breast cancer risk in the 12p11 locus in women of European ancestry

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

Signal

SNPs

Position (hg 19)

Alleles

EAF

LD (r 2)b

Univariate analysis

Conditional analysis

SNPs retained for functional annotatione

Per-allele OR (95 % CI)c

P-trend

Per-allele OR (95 % CI)d

P-trend

2

Indexa rs10771399

28155080

G*/A

0.12

-

0.85 (0.83–0.88)

5 × 10-25

-

-

-

1

rs7297051

28174817

T*/C

0.24

0.42

0.88 (0.86–0.90)

4 × 10-28

0.92 (0.89–0.94)

3 × 10-9

rs812020, chr12:28164044, rs2619434, rs2590275

2

rs805510

28139846

T*/C

0.12

0.88

0.85 (0.82–0.88)

10-25

0.93 (0.89–0.96)

2 × 10-5

74 SNPsf

3

rs1871152

28379826

G*/A

0.31

0.04

0.94 (0.92–0.96)

3 × 10-8

0.96 (0.94–0.98)

2 × 10-4

376 SNPsg

  1. *Effect alleles. aIdentified in the initial genome-wide association study conducted in women of European descent [1]. bLinkage disequilibrium (LD) with rs10771399 for women of European descent. cAdjusted for studies, and the top principal components and an additional principal component accounting for the Leuven Multidisciplinary Breast Centre (LMBC) study. dIncluded all three variants, and was adjusted for studies, and the top eight principal components as well as an additional principal component accounting for the LMBC study. eAssociated single nucleotide polymorphisms (SNPs) with a likelihood ratio >1/100 relative to the lead SNP in each signal. fSee Table S2 in Additional file 5. gSee Table S2 in Additional file 5. EAF effect allele frequency in controls, OR odds ratio, CI confidence interval
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Breast Cancer Research

ISSN: 1465-542X

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