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Table 1 Association of previously identified loci with breast cancer risk in 2,257 cases and 2,052 controls in the Seoul Breast Cancer Study

From: A genome-wide association study identifies a breast cancer risk variant in ERBB4 at 2q34: results from the Seoul Breast Cancer Study

Region/Reported gene(s) SNP Loci evaluated in this study Loci reported in genome-wide association studies
   Risk allele RAF OR (95% CI)a P Genotyping Risk allele RAF OR (95% CI) P Reference
1p11.2/NOTCH2, FCGR1B rs11249433 C 0.04 1.11 (0.88-1.40) 3.8 × 10-1 Imputed C 0.39 1.16 (1.09-1.24) 7 × 10-10 [8]
2q35/Intergenic rs13387042 A 0.10 1.11 (0.96-1.28) 1.6 × 10-1 Imputed A 0.50 1.2 (1.14-1.26) 1 × 10-13 [6]
3p24.1/SLC4A7 rs4973768 T 0.22 1.09 (0.98-1.21) 1.2 × 10-1 Imputed T 0.47 1.16 (1.10-1.24) 6 × 10-7 [9]
5q11.2/MAP3K1 rs16886165 G 0.35 1.14 (1.04-1.25) 6.5 × 10-3 Imputed G 0.15 1.23 (1.12-1.35) 5 × 10-7 [8]
  rs889312 C 0.55 1.16 (1.06-1.27) 8.5 × 10-4 Imputed C 0.28 1.13 (1.10-1.16) 7 × 10-20 [5]
5p12/MRPS30 rs7716600 A 0.48 1.13 (1.03-1.23) 6.9 × 10-3 Imputed A 0.23 1.24 (1.14-1.34) 7 × 10-7 [34]
  rs4415084 T 0.56 1.09 (0.99-1.19) 7.8 × 10-2 Imputed T 0.42 1.17 (1.11-1.22) 8 × 10-11 [24]
5p15.2/ROPN1L rs1092913 G 0.30 1.11 (1.01-1.22) 2.8 × 10-2 Imputed T 0.13 1.45 (1.24-1.69) 2 × 10-6 [35]
6q22.33/ECHDC1, RNF146 rs2180341 G 0.27 1.03 (0.93-1.13) 6.0 × 10-1 Typed G 0.21 1.41 (1.25-1.59) 3 × 10-8 [36]
6q25.1/ESR1, C6orf97 rs3734805 C 0.33 1.20 (1.09-1.33) 1.8 × 10-4 Imputed C 0.08 1.19 (1.11-1.27) 1 × 10-7 [24]
  rs2046210 A 0.35 1.29 (1.18-1.41) 5.8 × 10-8 Typed A 0.37 1.29 (1.21-1.37) 2 × 10-15 [10]
7q32.3/NR rs2048672 C 0.49 1.05 (0.97-1.15) 2.3 × 10-1 Typed C 0.45 1.11 (1.05-1.17) 6 × 10-6 [12]
8q24.21/Intergenic rs13281615 C 0.57 1.04 (0.95-1.14) 3.8 × 10-1 Imputed C 0.40 1.08 (1.05-1.11) 5 × 10-12 [5]
  rs1562430 T 0.87 1.16 (1.01-1.33) 3.0 × 10-2 Imputed T 0.58 1.17 (1.10-1.25) 6 × 10-7 [9]
9p21.3/CDKN2A, CDKN2B rs1011970 T 0.07 1.00 (0.84-1.19) 9.9 × 10-1 Imputed T 0.17 1.09 (1.04-1.14) 3 × 10-8 [9]
9q31.2/KLF4, RAD23B, ACTL7A rs865686 T 0.93 1.02 (0.86-1.21) 8.1 × 10-1 Imputed T 0.61 1.12 (1.09-1.18) 2 × 10-10 [24]
10p15.1/ANKRD16, FBXO18 rs2380205 C 0.91 1.11 (0.95-1.29) 1.8 × 10-1 Typed C 0.57 1.06 (1.02-1.10) 5 × 10-7 [9]
10q21.2/ZNF365 rs10995190 G 0.98 1.02 (0.76-1.38) 8.9 × 10-1 Imputed G 0.85 1.16 (1.10-1.22) 5 × 10-15 [9]
  rs10822013 T 0.47 1.06 (0.97-1.15) 2.1 × 10-1 Typed T 0.47 1.12 (1.06-1.18) 6 × 10-9 [12]
10q22.3/ZMIZ1 rs704010 A 0.29 1.08 (0.98-1.19) 1.2 × 10-1 Typed A 0.39 1.07 (1.03-1.11) 4 × 10-9 [9]
10q26.13/FGFR2 rs10510102 G 0.18 1.01 (0.90-1.13) 8.4 × 10-1 Typed G 0.17 1.12 (1.07-1.17) 2 × 10-6 [24]
  rs10736303b G 0.53 1.17 (1.07-1.28) 4.4 × 10-4 Typed T 0.41 1.17 (1.07-1.27) 2 × 10-10 [8]
11p15.5/LSP1 rs3817198 C 0.16 1.00 (0.89-1.13) 9.5 × 10-1 Typed C 0.30 1.07 (1.04-1.11) 3 × 10-9 [5]
14q24.1/RAD51L1 rs10483813c T 0.97 1.21 (0.93-1.56) 1.6 × 10-1 Imputed C 0.76 1.06 (1.01-1.14) 2 × 10-7 [8]
16q12.1/TOX3 rs4784227 T 0.29 1.27 (1.15-1.40) 1.5 × 10-6 Typed T 0.24 1.24 (1.20-1.29) 1 × 10-28 [11]
  rs3803662 T 0.64 1.24 (1.14-1.36) 2.4 × 10-6 Typed T 0.27 1.28 (1.21-1.35) 6 × 10-19 [5]
19q13.41/ZNF577 rs10411161 C 0.72 1.01 (0.92-1.11) 8.6 × 10-1 Typed T 0.13 1.42 (1.22-1.65) 7 × 10-6 [35]
  1. The average call rate was 99.8% (range of 99.4% to 100%) for typed single-nucleotide polymorphisms (SNPs), and the average of imputation quality score from MACH (r2) was 0.97 (range of 0.95 to 1.00). aPer-allele odds ratio (OR) adjusted for age; bproxy SNP of rs2981579 (r2 = 0.48 in CHB+JPT; r2 = 0.74 in CEU); cproxy SNP of rs999737 (r2 = 0.50 in CHB+JPT; r2 = 0.98 in CEU). CEU, CEPH Utah residents with ancestry from Northern and Western Europe; CHB+JPT, Han Chinese from Beijing + Japanese from Tokyo; CI, confidence interval; RAF, risk allele frequency.