Skip to main content

Table 1 Association of breast cancer risk with 15 SNPs selected from previous GWAS study in the Testing Set.

From: Breast cancer risk assessment with five independent genetic variants and two risk factors in Chinese women

SNP Chr.
(Cytoband)
Position Associated genes GWAS study Allelesa Call
Rate
(%)
P b MAFc MAFd Case (%) Control (%) P e
rs13387042 2q35 217614077 TNP1, IGFBP5,
IGFBP2
Stacey, 2007 (12)
Thomas, 2009 (13)
G > A 98.65 0.41 0.11 0.12 1.39/25.87/72.74 1.01/21.08/77.91 0.039
rs4973768 3p24.1 27391017 SLC4A7 Ahmed, 2009 (8) C > T 97.58 0.91 0.17 0.19 3.05/35.05/61.90 3.63/31.52/64.85 0.265
rs2307032 3p24.1 27407999 SLC4A7 Ahmed, 2009 (8) C > T 97.92 0.08 0.41 0.40 18.58/50.64/30.78 17.61/45.23/37.16 0.017
rs16886165 5p11.2 56058840 MAP3K1 Thomas, 2009 (13) T > G 96.34 0.65 0.31 0.34 12.10/46.98/40.93 11.49/45.98/42.53 0.781
rs889312 5q11.2 56067641 MAP3K1 Easton, 2007 (9) C > A 98.31 0.23 0.50 0.48 21.55/50.41/28.04 22.03/52.09/25.88 0.595
rs4415084 5p12 44698272 Unknown Stacey, 2008 (12)
Thomas,2009 (13)
A > G 96.12 0.03 0.46 0.43 19.95/44.56/35.84 20.41/45.64/33.94 0.798
rs10941679 5p12 44742255 MRPS30 Stacey, 2008 (12)
Thomas,2009 (13)
G > A 97.19 0.95 0.57 0.50 24.23/49.29/26.48 24.83/50.23/24.94 0.768
rs2180341 6q22.33 127642323 ECHDC1, RNF146 Gold, 2008 (10) A > G 97.30 0.49 0.22 0.26 6.35/43.88/49.76 7.50/37.95/54.55 0.040
rs2046210 6q25.1 151990059 ESR1, C6orf97 Zheng, 2009 (14) G > A 98.48 0.50 0.35 0.34 18.35/47.97/33.68 12.36/44.16/43.48 1.26 × 10-5
rs13281615 8q24.21 128424800 Unknown Easton, 2007 (9) A > G 97.98 0.59 0.57 0.49 23.56/52.40/24.03 24.63/49.04/26.32 0.353
rs1562430 8q24.21 128457034 Unknown Thomas 2009 (13) T > C 98.82 0.11 0.20 0.18 2.75/27.38/69.87 2.49/31.33/66.18 0.191
rs2981582 10q26.13 123342307 FGFR2 Easton, 2007 (9) C > T 99.44 0.94 0.33 0.31 12.61/45.87/41.51 9.82/43.3/46.88 0.037
rs3817198 11p15.5 1865582 LSP1 Easton, 2007 (9) T > C 98.82 0.88 0.09 0.12 2.41/23.79/73.79 1.58/21.53/76.89 0.213
rs12443621 16q12.1 51105538 TNRC9 Easton, 2007 (9) G > A 99.10 0.34 0.39 0.45 18.23/48.17/33.60 19.10/51.12/29.78 0.227
rs6504950 17q23.2 50411470 COX11 Ahmed, 2009 (8) G > A 98.71 0.84 0.10 0.09 0.35/14.14/85.52 0.78/15.92/83.30 0.264
  1. a Major > Minor; b P-values for Hardy-Weinberg equilibrium(HWE) in the controls by exact test; c Minor Allele Frequency (MAF) of Chinese Han population from Beijing (CHB) based on the International HapMap project (Phase II+III, rel 27); d Minor Allele Frequency (MAF) in controls; e P-values for genotypic frequency between cases and controls by Fisher's exact test.