Table 1.
Breast cancer association results
| Region | Index SNP (locus) | Chromosome | Length (Mbp) | SNV MAF ≤0.005 | SNV MAF >0.005 | High-impact SNVsb | p value (index SNP) | p value (top SNP) | Conditional analysis on top SNP p value (top SNP) | Conditional analysis on index SNP p value (top SNP) |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | rs13387042 (2q35) | 2 | 0.122 | 3469 | 674 | 0 | 0.00016 | 2.68E-05 (rs6721996) | 0.0070 (rs116670542) | 0.0066 (rs116670542) |
| 2 | rs10069690 (TERT) | 5 | 0.046 | 1681 | 167 | 0 | 0.0044 | 0.0044 (rs10069690) | 0.025 (rs34768248) | 0.025 (rs34768248) |
| 3 | rs889312 (MAP3K1) | 5 | 0.308 | 6663 | 986 | 4 | 0.098 | 0.00035 (rs111944656) | 0.0022 (rs79128470) | 0.0021 (rs111944656) |
| 4 | rs2046210a (ESR1) | 6 | 0.243 | 4209 | 727 | 10 | 0.015 | 0.00023 (rs9383938) | 0.0074 (rs80347946) | 0.0077 (rs80347946) |
| 5 | rs1562430 (8q24) | 8 | 0.973 | 20,730 | 3260 | 5 | 0.18 | 9.87E-05 (rs112613843) | 0.00020 (rs4871810) | 0.00019 (rs4871841) |
| 6 | rs10995190 (ZNF365) | 10 | 0.876 | 7635 | 1056 | 1 | 0.76 | 2.7E-05 (rs12570941) | 0.0085 (rs73282644) | 5.39E-05 (rs12570941) |
| 7 | rs704010 (ZMIZ1) | 10 | 0.398 | 13,622 | 1822 | 4 | 0.019 | 0.00025 (Chr10-81107117) | 0.00076 (rs117770051) | 0.00019 (Chr10-81107117) |
| 8 | rs2981579 (FGFR2) | 10 | 0.473 | 20,081 | 3033 | 15 | 0.00046 | 4.42E-05 (rs10736303) | 0.00020 (rs192776427) | 0.00024 (rs192776427) |
| 9 | rs614367 (11q13) | 11 | 0.259 | 6743 | 1010 | 5 | 0.75 | 2.15E-06 (rs61041893) | 0.00032 (rs11823311) | 5.47E-05 (rs598003) |
| 10 | rs999737 (RAD51B) | 14 | 0.815 | 15,992 | 2025 | 8 | 0.067 | 0.00050 (rs76904544) | 0.00086 (rs113627141) | 0.00074 (rs113627141) |
| 11 | rs3803662 (TOX3) | 16 | 0.269 | 7337 | 910 | 0 | 0.036 | 0.00013 (rs12922061) | 0.0013 (rs8048809) | 0.0013 (rs4784227) |
| 12 | rs8170 (MERIT40) | 19 | 0.712 | 13,080 | 1880 | 31 | 0.67 | 0.0035 (rs62126223) | 0.0069 (rs117673644) | 0.0035 (rs62126223) |
MAF Minor allele frequency, SNP Single-nucleotide polymorphism, SNV Single-nucleotide variant
The results shown are derived from genome-wide association study index single-nucleotide polymorphisms and best associated single-nucleotide variant in sequenced regions spanning 12 breast cancer genome-wide association study loci. Results are also shown for conditional analysis adjusted for either best associated (“top”) SNP or the original index genome-wide association study SNP
aSNP was filtered in quality control, p value for rs12662670
bAs defined by SnpEff [43]