Table 2 Association analysis of novel SNPs in cross-ancestry combined meta-analysis by estrogen receptor status.

From: Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women

       

ER positive

ER negative

P for heterogeneitya

SNP

Chr

Position

Test

Other

Locus

Nearest genes

TAF

OR (95% CI)

P value

TAF

OR (95% CI)

P value

rs17024629

1

110,179,756

T

C

1p13.3

GSTM4, AMPD2, GSTM2, GSTM1, GNAT2, MIR197, GNAI3

0.16

0.95 (0.93–0.97)

1.1E−06

0.16

0.95 (0.93–0.98)

0.0014

0.96

rs67931591

1

215,330,292

G

GCTGAGG-

CAGGAGA

1q41

KCNK2, KCTD3, CENPF

0.66

0.98 (0.96–0.99)

0.0020

0.65

0.94 (0.92–0.96)

4.3E−08

0.003

rs2522057

5

131,801,947

C

G

5q31.1

C5orf56, IRF1, SLC22A5, IL5, RAD50

0.60

0.96 (0.95–0.98)

2.9E−07

0.60

0.98 (0.96–1.01)

0.14

0.011

rs1637365

7

74,359,358

T

C

7q11.23

GTF2IRD2, STAG3L2, PMS2P5, WBSCR16

0.30

1.02 (1.00–1.04)

0.026

0.32

1.08 (1.05–1.11)

1.0E−08

3.9E−04

rs1869959

15

75,147,332

A

C

15q24.1

CSK, CYP1A2, ULK3, MPI, SCAMP2, CPLX3, ARID3B, PTPN9

0.30

0.96 (0.94–0.97)

6.0E−08

0.31

0.96 (0.94–0.99)

0.0022

0.64

rs60381548

15

75,728,474

CA

C

15q24.2

PTPN9, SCAMP5, C15orf39, COMMD4, SIN3A, SNUPN

0.27

0.96 (0.95–0.98)

1.1E−05

0.28

0.95 (0.93–0.98)

1.7E−04

0.47

rs181337095

15

100,907,094

A

G

15q26.3

ADAMTS17, PCSK6

0.85

1.05 (1.03–1.08)

1.1E−05

0.83

1.06 (1.03–1.10)

2.9E−04

0.60

  1. TAF Test allele frequency, SNP single nucleotide polymorphism, OR odds ratio, CI confidence intervals.
  2. aP for heterogeneity between ER-positive and ER-negative tumors.
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