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Table 1 Breast cancer association results

From: Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities

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)
  1. MAF Minor allele frequency, SNP Single-nucleotide polymorphism, SNV Single-nucleotide variant
  2. 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
  3. aSNP was filtered in quality control, p value for rs12662670
  4. bAs defined by SnpEff [43]
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