Table 1

Results from univariate replication analysis on full dataset: single nucleotide polymorphisms (SNPs) given with frequency of risk allele (RAF), genotyping call rate (cr), per-allele OR for breast cancer with 95%CI, for breast cancer overall and for ER− and ER+ tumours alone

AllER+ER−
Geners-numberChrPositionRAFcrOR95% CIOR95% CIOR95% CI
NOTCH2rs11249433*11209821360.4298.31.09(1.04 to 1.15)1.13(1.07 to 1.20)1.00(0.89 to 1.12)
CASP8rs10931936‡22018521730.2997.01.08(1.03 to 1.13)1.04(0.98 to 1.11)1.10(0.97 to 1.25)
CASP8rs1045485*22018578340.8798.11.13(1.05 to 1.21)1.13(1.03 to 1.23)1.12(0.95 to 1.32)
Intergenicrs13387042*22176140770.5398.21.20(1.15 to 1.26)1.26(1.19 to 1.34)1.05(0.94 to 1.17)
SLC4A7rs4973768*3273910170.4998.71.08(1.04 to 1.14)1.09(1.03 to 1.15)0.97(0.87 to 1.08)
TERTrs10069690*512797900.2697.01.04(0.99 to 1.09)1.04(0.97 to 1.11)1.18(1.05 to 1.34)
Intergenicrs4415084‡5446982720.4197.91.08(1.03 to 1.13)1.11(1.04 to 1.17)1.02(0.91 to 1.14)
Intergenicrs10941679*5447422550.2697.31.12(1.07 to 1.18)1.16(1.08 to 1.23)1.03(0.91 to 1.17)
MAP3K1rs889312*5560676410.2998.41.11(1.06 to 1.17)1.14(1.07 to 1.22)1.02(0.90 to 1.15)
ECHDC1/RNF146rs218034161276423230.7698.11.03(0.98 to 1.09)1.02(0.96 to 1.10)1.01(0.89 to 1.15)
C6orf97 (ESR1)rs938393561519398480.0957.41.11(1.01 to 1.22)1.12(0.99 to 1.26)0.96(0.73 to 1.26)
Intergenicrs375731861519558060.0898.21.13(1.04 to 1.22)1.16(1.04 to 1.28)1.07(0.87 to 1.33)
Intergenicrs938393861519873570.0999.01.12(1.04 to 1.21)1.15(1.05 to 1.27)1.12(0.92 to 1.37)
Intergenicrs2046210†61519900590.3598.41.09(1.04 to 1.14)1.10(1.04 to 1.17)1.07(0.96 to 1.20)
Intergenicrs1328161581284248010.4298.11.08(1.03 to 1.14)1.09(1.02 to 1.15)1.08(0.96 to 1.20)
Intergenicrs1562430*81284570340.5998.91.12(1.07 to 1.17)1.16(1.09 to 1.22)1.13(1.01 to 1.27)
CDKN2B-AS1rs10119709220521340.1798.51.07(1.01 to 1.14)1.00(0.93 to 1.08)1.02(0.88 to 1.18)
Intergenicrs865686*91108884780.6498.61.10(1.05 to 1.15)1.10(1.04 to 1.16)1.20(1.07 to 1.35)
Intergenicrs2380205*1059267400.5698.81.05(1.01 to 1.10)1.04(0.98 to 1.10)1.04(0.92 to 1.16)
ZNF365rs10995190*10639486880.8698.21.12(1.05 to 1.19)1.12(1.04 to 1.21)1.06(0.90 to 1.26)
ZNF365rs1691730210642611980.9197.51.04(0.97 to 1.12)1.06(0.97 to 1.16)0.97(0.80 to 1.18)
ZMIZ1rs1250003*‡10808468140.3997.01.04(1.00 to 1.09)1.05(0.99 to 1.11)0.98(0.87 to 1.10)
FGFR2rs3750817101233225670.6197.71.16(1.11 to 1.22)1.18(1.11 to 1.26)1.03(0.92 to 1.15)
FGFR2rs2981582*101233423080.4198.11.22(1.17 to 1.28)1.24(1.17 to 1.31)1.09(0.97 to 1.22)
LSP1rs38171981118655830.6897.71.01(0.97 to 1.07)1.01(0.95 to 1.07)1.07(0.95 to 1.20)
LSP1rs9091161118985220.5398.81.04(1.00 to 1.09)1.05(0.99 to 1.10)0.99(0.89 to 1.11)
Intergenicrs614367*11690379450.1599.21.15(1.08 to 1.22)1.18(1.10 to 1.27)0.98(0.83 to 1.15)
RAD51L1rs999737*‡14681044350.7798.71.12(1.06 to 1.18)1.14(1.07 to 1.22)1.05(0.92 to 1.20)
TNRC9rs3803662*16511438430.2998.21.20(1.14 to 1.26)1.18(1.11 to 1.26)1.19(1.05 to 1.34)
COL1A1rs207555517456292900.1498.81.04(0.97 to 1.11)1.05(0.97 to 1.14)1.14(0.97 to 1.34)
COX11rs6504950*17504114700.7398.91.08(1.02 to 1.14)1.10(1.03 to 1.17)1.08(0.96 to 1.23)
GMEB2rs31149920622175890.9397.21.03(0.94 to 1.12)1.05(0.94 to 1.17)0.96(0.76 to 1.20)
  • *These 18 SNPs were selected as independent effects into common model.

  • †SNP selected on basis of common model on four SNPs in that region.

  • ‡For some cohorts genotypes not from this SNP but from surrogate marker with r2≥0.98.

  • ER, oestrogen receptor.