Table 3.
Odds ratios and 95% posterior intervals for the association between the selected single nucleotide polymorphisms (SNPs) and each breast cancer subtype, relative to controls [SNP log OR~N(0,τ2), τ2 ~ Γ−1(4, 0.5) with mode=0.10]a
| Gene | SNP | Luminal A N=700 |
Luminal B N=122 |
HER2+/ER− N=98 |
Unclassified N=133 |
Basal-like N=207 |
|---|---|---|---|---|---|---|
| 1p12 | rs11249433 | 1.09 (0.94, 1.25) | 1.04 (0.78, 1.33) | 1.11 (0.79, 1.45) | 1.24 (0.93, 1.58) | 1.09 (0.85, 1.35) |
| CASP8 | rs1045485 | 1.10 (0.88, 1.32) | 1.00 (0.67, 1.35) | 0.97 (0.62, 1.33) | 1.24 (0.80, 1.73) | 1.15 (0.80, 1.56) |
| CASP8 | rs17468277 | 1.11 (0.89, 1.35) | 0.96 (0.64, 1.34) | 0.94 (0.60, 1.32) | 1.29 (0.84, 1.82) | 1.10 (0.79, 1.47) |
| 2q35 | rs13387042 | 1.18 (1.04, 1.35) | 0.99 (0.76, 1.25) | 0.98 (0.69, 1.25) | 1.10 (0.85, 1.40) | 0.92 (0.73, 1.12) |
| 2p | rs4666451 | 0.97 (0.85, 1.11) | 1.03 (0.76, 1.29) | 1.14 (0.84, 1.48) | 1.24 (0.93, 1.56) | 1.16 (0.91, 1.41) |
| SLC4A7 | rs4973768 | 0.98 (0.86, 1.09) | 1.01 (0.78, 1.27) | 0.91 (0.68, 1.17) | 0.93 (0.70, 1.15) | 0.99 (0.78, 1.19) |
| 4p | rs12505080 | 1.18 (1.02, 1.36) | 1.14 (0.84, 1.45) | 1.15 (0.82, 1.54) | 0.88 (0.61, 1.13) | 0.98 (0.75, 1.21) |
| TLR1 | rs7696175 | 1.20 (1.02, 1.38) | 0.99 (0.74, 1.29) | 0.79 (0.54, 1.04) | 1.08 (0.77, 1.38) | 1.27 (0.96, 1.59) |
| MRPS30 | rs4415084 | 1.11 (0.96, 1.25) | 1.06 (0.80, 1.32) | 1.15 (0.85, 1.49) | 1.08 (0.84, 1.35) | 1.17 (0.93, 1.41) |
| MRPS30 | rs10941679 | 1.10 (0.93, 1.27) | 0.94 (0.69, 1.22) | 1.04 (0.73, 1.36) | 0.95 (0.69, 1.23) | 1.21 (0.95, 1.45) |
| 5p12 | rs981782 | 0.90 (0.78, 1.03) | 0.88 (0.64, 1.12) | 1.08 (0.78, 1.41) | 0.99 (0.72, 1.28) | 1.07 (0.82, 1.33) |
| 5q | rs30099 | 1.09 (0.89, 1.31) | 1.03 (0.66, 1.37) | 1.13 (0.75, 1.56) | 0.91 (0.60, 1.20) | 0.99 (0.73, 1.28) |
| MAP3K1 | rs889312 | 1.17 (1.02, 1.33) | 1.04 (0.80, 1.32) | 1.00 (0.74, 1.30) | 1.08 (0.82, 1.35) | 0.89 (0.70, 1.09) |
| ESR1 | rs2046210 | 1.03 (0.90, 1.16) | 1.07 (0.82, 1.36) | 1.29 (0.97, 1.67) | 1.15 (0.88, 1.44) | 1.29 (1.01, 1.55) |
| ESR1 | rs851974 | 0.89 (0.77, 1.02) | 1.13 (0.84, 1.43) | 0.86 (0.62, 1.12) | 0.88 (0.64, 1.10) | 0.96 (0.76, 1.18) |
| ESR1 | rs2077647 | 0.95 (0.83, 1.08) | 1.00 (0.76, 1.25) | 0.98 (0.72, 1.26) | 0.94 (0.71, 1.16) | 0.96 (0.76, 1.17) |
| ESR1 | rs2234693 | 0.91 (0.79, 1.04) | 0.96 (0.75, 1.20) | 1.02 (0.75, 1.27) | 0.86 (0.67, 1.08) | 0.99 (0.79, 1.18) |
| ESR1 | rs1801132 | 1.09 (0.92, 1.28) | 0.91 (0.66, 1.20) | 0.98 (0.67, 1.31) | 1.02 (0.74, 1.32) | 0.85 (0.64, 1.05) |
| ESR1 | rs3020314 | 1.02 (0.89, 1.17) | 1.23 (0.93, 1.54) | 1.08 (0.80, 1.37) | 0.99 (0.77, 1.23) | 1.12 (0.90, 1.34) |
| ESR1 | rs3798577 | 0.97 (0.86, 1.10) | 1.05 (0.79, 1.32) | 0.82 (0.62, 1.02) | 1.10 (0.85, 1.35) | 1.00 (0.82, 1.21) |
| ECHDC1 | rs2180341 | 0.99 (0.84, 1.13) | 1.01 (0.75, 1.31) | 1.04 (0.74, 1.36) | 0.95 (0.70, 1.20) | 1.01 (0.80, 1.23) |
| RELN | rs17157903 | 1.00 (0.83, 1.18) | 1.07 (0.74, 1.41) | 0.77 (0.48, 1.09) | 0.99 (0.70, 1.32) | 1.09 (0.78, 1.39) |
| 8q24 | rs13281615 | 1.04 (0.90, 1.17) | 0.99 (0.75, 1.25) | 1.13 (0.85, 1.43) | 1.08 (0.85, 1.35) | 0.98 (0.79, 1.17) |
| 8q24 | rs1562430 | 1.06 (0.93, 1.19) | 0.96 (0.72, 1.22) | 1.20 (0.90, 1.55) | 1.06 (0.83, 1.32) | 1.07 (0.85, 1.28) |
| CDKN2A/B | rs3731257 | 0.92 (0.78, 1.06) | 0.89 (0.64, 1.17) | 0.96 (0.66, 1.26) | 0.91 (0.66, 1.19) | 0.91 (0.70, 1.16) |
| CDKN2A/B | rs3731249 | 0.99 (0.65, 1.33) | 1.08 (0.55, 1.68) | 1.11 (0.56, 1.76) | 0.95 (0.49, 1.46) | 0.96 (0.51, 1.48) |
| CDKN2A/B | rs518394 | 0.99 (0.86, 1.13) | 1.00 (0.73, 1.26) | 0.77 (0.52, 1.00) | 1.04 (0.76, 1.34) | 1.14 (0.88, 1.38) |
| CDKN2A/B | rs564398 | 1.01 (0.85, 1.15) | 1.01 (0.76, 1.28) | 0.81 (0.56, 1.08) | 1.08 (0.80, 1.40) | 1.09 (0.83, 1.36) |
| CDKN2A/B | rs1011970 | 1.12 (0.96, 1.29) | 0.91 (0.65, 1.15) | 0.90 (0.63, 1.15) | 0.87 (0.63, 1.10) | 1.12 (0.86, 1.38) |
| CDKN2A/B | rs10757278 | 1.05 (0.90, 1.18) | 1.06 (0.80, 1.35) | 1.02 (0.75, 1.31) | 1.22 (0.93, 1.52) | 1.10 (0.86, 1.34) |
| CDKN2A/B | rs10811661 | 0.95 (0.78, 1.13) | 1.01 (0.71, 1.35) | 0.82 (0.54, 1.15) | 0.84 (0.56, 1.12) | 1.10 (0.81, 1.39) |
| ANKRD16 | rs2380205 | 1.03 (0.90, 1.15) | 1.05 (0.79, 1.30) | 1.10 (0.82, 1.40) | 0.80 (0.61, 0.99) | 0.94 (0.77, 1.13) |
| ZNF365 | rs10995190 | 1.03 (0.84, 1.22) | 0.83 (0.59, 1.09) | 0.83 (0.59, 1.11) | 1.24 (0.88, 1.64) | 0.95 (0.74, 1.21) |
| ZMIZ1 | rs704010 | 1.09 (0.94, 1.25) | 1.34 (0.96, 1.70) | 1.36 (0.97, 1.77) | 0.96 (0.70, 1.25) | 1.34 (1.03, 1.66) |
| FGFR2 | rs1896395 | 1.05 (0.80, 1.30) | 0.92 (0.54, 1.33) | 1.31 (0.73, 1.89) | 1.06 (0.70, 1.44) | 1.06 (0.71, 1.40) |
| FGFR2 | rs3750817 | 1.33 (1.13, 1.53) | 1.27 (0.92, 1.64) | 1.22 (0.86, 1.60) | 1.26 (0.92, 1.64) | 1.01 (0.79, 1.25) |
| FGFR2 | rs10736303 | 1.32 (1.14, 1.52) | 1.31 (0.98, 1.65) | 1.26 (0.90, 1.64) | 1.37 (0.99, 1.77) | 0.99 (0.78, 1.22) |
| FGFR2 | rs11200014 | 1.26 (1.10, 1.43) | 1.05 (0.80, 1.31) | 1.19 (0.86, 1.52) | 1.41 (1.08, 1.77) | 0.88 (0.70, 1.07) |
| FGFR2 | rs2981579 | 1.26 (1.10, 1.42) | 1.11 (0.84, 1.41) | 1.34 (1.00, 1.68) | 1.44 (1.11, 1.80) | 0.92 (0.74, 1.10) |
| FGFR2 | rs1078806 | 1.24 (1.08, 1.42) | 1.07 (0.79, 1.36) | 1.19 (0.86, 1.53) | 1.40 (1.06, 1.76) | 0.87 (0.68, 1.07) |
| FGFR2 | rs2981578 | 1.33 (1.15, 1.51) | 1.31 (1.01, 1.67) | 1.34 (0.98, 1.76) | 1.38 (1.03, 1.84) | 1.01 (0.79, 1.25) |
| FGFR2 | rs1219648 | 1.29 (1.13, 1.47) | 1.10 (0.83, 1.37) | 1.24 (0.89, 1.59) | 1.62 (1.24, 2.04) | 0.95 (0.76, 1.15) |
| FGFR2 | rs2912774 | 1.26 (1.10, 1.41) | 1.11 (0.84, 1.39) | 1.42 (1.06, 1.80) | 1.47 (1.14, 1.85) | 0.92 (0.73, 1.09) |
| FGFR2 | rs2936870 | 1.26 (1.09, 1.41) | 1.13 (0.86, 1.43) | 1.38 (1.02, 1.76) | 1.50 (1.16, 1.89) | 0.91 (0.72, 1.09) |
| FGFR2 | rs2420946 | 1.22 (1.06, 1.38) | 1.06 (0.80, 1.32) | 1.40 (1.04, 1.79) | 1.46 (1.12, 1.83) | 0.89 (0.71, 1.07) |
| FGFR2 | rs2162540 | 1.28 (1.11, 1.45) | 1.08 (0.82, 1.36) | 1.42 (1.05, 1.83) | 1.52 (1.17, 1.90) | 0.91 (0.72, 1.10) |
| FGFR2 | rs2981582 | 1.27 (1.09, 1.43) | 1.10 (0.87, 1.40) | 1.39 (1.02, 1.76) | 1.28 (1.00, 1.57) | 0.92 (0.73, 1.10) |
| FGFR2 | rs3135718 | 1.26 (1.10, 1.42) | 1.13 (0.85, 1.40) | 1.35 (1.01, 1.71) | 1.51 (1.17, 1.90) | 0.91 (0.73, 1.09) |
| 10q | rs10510126 | 1.09 (0.88, 1.30) | 1.07 (0.73, 1.46) | 1.08 (0.72, 1.49) | 0.94 (0.63, 1.26) | 1.14 (0.81, 1.48) |
| ATM | rs1800054 | 1.10 (0.66, 1.59) | 1.10 (0.54, 1.76) | 1.12 (0.51, 1.78) | 1.00 (0.49, 1.62) | 1.20 (0.58, 1.91) |
| ATM | rs1800057 | 1.19 (0.81, 1.64) | 0.95 (0.49, 1.48) | 1.33 (0.68, 2.13) | 1.01 (0.50, 1.60) | 1.10 (0.56, 1.67) |
| ATM | rs1800058 | 1.05 (0.67, 1.44) | 0.94 (0.45, 1.46) | 1.03 (0.51, 1.67) | 0.98 (0.47, 1.56) | 0.98 (0.49, 1.56) |
| ATM | rs1801516 | 1.03 (0.82, 1.24) | 1.05 (0.70, 1.43) | 0.97 (0.64, 1.37) | 0.95 (0.63, 1.32) | 0.99 (0.70, 1.32) |
| ATM | rs3092992 | 0.97 (0.68, 1.30) | 0.99 (0.57, 1.49) | 1.19 (0.62, 1.85) | 1.05 (0.61, 1.57) | 1.38 (0.79, 1.97) |
| ATM | rs664143 | 1.09 (0.95, 1.23) | 1.00 (0.77, 1.25) | 1.06 (0.79, 1.35) | 0.94 (0.74, 1.17) | 0.98 (0.79, 1.19) |
| ATM | rs170548 | 0.98 (0.84, 1.13) | 0.90 (0.66, 1.16) | 1.00 (0.72, 1.31) | 0.94 (0.69, 1.22) | 1.00 (0.77, 1.24) |
| ATM | rs3092993 | 1.03 (0.83, 1.25) | 1.06 (0.69, 1.48) | 0.94 (0.60, 1.35) | 0.96 (0.61, 1.29) | 1.03 (0.73, 1.37) |
| LSP1 | rs3817198 | 1.02 (0.88, 1.18) | 0.87 (0.62, 1.10) | 1.19 (0.86, 1.52) | 1.21 (0.92, 1.55) | 1.02 (0.79, 1.26) |
| LSP1 | rs909116 | 1.09 (0.94, 1.23) | 0.92 (0.69, 1.15) | 1.23 (0.90, 1.58) | 1.03 (0.79, 1.30) | 1.09 (0.86, 1.32) |
| H19 | rs2107425 | 1.03 (0.90, 1.17) | 0.93 (0.71, 1.17) | 0.99 (0.74, 1.24) | 0.94 (0.72, 1.18) | 1.00 (0.81, 1.19) |
| TNRC9/TOX3 | rs16951186 | 1.02 (0.78, 1.25) | 1.30 (0.79, 1.88) | 0.84 (0.48, 1.21) | 0.83 (0.52, 1.12) | 0.97 (0.67, 1.31) |
| TNRC9/TOX3 | rs8051542 | 1.10 (0.97, 1.24) | 0.96 (0.74, 1.20) | 1.12 (0.84, 1.43) | 1.31 (1.02, 1.64) | 0.84 (0.66, 1.03) |
| TNRC9/TOX3 | rs12443621 | 1.06 (0.94, 1.20) | 0.93 (0.71, 1.16) | 1.21 (0.92, 1.55) | 0.95 (0.74, 1.18) | 1.00 (0.82, 1.21) |
| TNRC9/TOX3 | rs3803662 | 1.16 (1.01, 1.33) | 1.09 (0.83, 1.35) | 1.01 (0.77, 1.29) | 1.13 (0.88, 1.41) | 0.96 (0.78, 1.16) |
| TNRC9/TOX3 | rs4784227 | 1.32 (1.13, 1.54) | 1.09 (0.76, 1.43) | 1.10 (0.76, 1.46) | 1.29 (0.94, 1.67) | 0.90 (0.66, 1.17) |
| TNRC9/TOX3 | rs3104746 | 1.58 (1.24, 1.94) | 1.05 (0.60, 1.50) | 1.31 (0.80, 1.85) | 1.12 (0.76, 1.58) | 1.49 (1.06, 1.98) |
| TNRC9/TOX3 | rs3112562 | 1.07 (0.93, 1.22) | 0.88 (0.62, 1.14) | 1.46 (1.06, 1.87) | 0.80 (0.60, 1.03) | 1.33 (1.06, 1.62) |
| TNRC9/TOX3 | rs9940048 | 1.13 (0.97, 1.28) | 0.84 (0.61, 1.08) | 1.17 (0.86, 1.50) | 0.98 (0.72, 1.25) | 0.91 (0.72, 1.11) |
| TP53 | rs9894946 | 0.86 (0.72, 1.02) | 0.83 (0.59, 1.12) | 1.01 (0.65, 1.36) | 1.05 (0.71, 1.43) | 1.12 (0.81, 1.49) |
| TP53 | rs1614984 | 1.01 (0.88, 1.13) | 0.94 (0.71, 1.16) | 1.01 (0.78, 1.28) | 1.04 (0.79, 1.30) | 1.13 (0.92, 1.36) |
| TP53 | rs12951053 | 0.95 (0.75, 1.18) | 1.32 (0.86, 1.84) | 1.16 (0.71, 1.62) | 1.25 (0.82, 1.73) | 0.99 (0.70, 1.30) |
| TP53 | rs17880604 | 0.87 (0.49, 1.24) | 0.84 (0.35, 1.38) | 1.21 (0.54, 1.94) | 0.96 (0.46, 1.57) | 1.12 (0.57, 1.76) |
| TP53 | rs1800372 | 0.97 (0.55, 1.38) | 1.24 (0.57, 2.00) | 0.93 (0.39, 1.53) | 1.34 (0.59, 2.22) | 1.04 (0.46, 1.71) |
| TP53 | rs2909430 | 1.12 (0.96, 1.31) | 1.09 (0.78, 1.45) | 1.06 (0.73, 1.38) | 0.88 (0.63, 1.13) | 1.10 (0.85, 1.37) |
| TP53 | rs1042522 | 1.03 (0.89, 1.18) | 0.99 (0.73, 1.26) | 0.82 (0.61, 1.06) | 0.94 (0.70, 1.17) | 0.97 (0.77, 1.18) |
| TP53 | rs8079544 | 0.98 (0.78, 1.23) | 1.38 (0.83, 2.07) | 0.76 (0.45, 1.07) | 0.87 (0.59, 1.20) | 1.05 (0.71, 1.44) |
| COX11 | rs7222197 | 1.06 (0.92, 1.22) | 1.08 (0.80, 1.35) | 1.01 (0.74, 1.29) | 1.09 (0.82, 1.37) | 1.05 (0.85, 1.27) |
| COX11 | rs6504950 | 1.05 (0.91, 1.20) | 1.07 (0.80, 1.37) | 1.00 (0.73, 1.28) | 1.08 (0.81, 1.35) | 1.05 (0.84, 1.28) |
a
Estimates generated using polytomous logistic regression adjusting for age at diagnosis/selection, proportion African ancestry and self-reported race.