Table 3 Significant secondary associations identified around selected breast cancer CpGs through conditional analysis of predictor meQTL SNPs.
CpG | Chr | Location (bp) | Cytoband | meQTL SNP | Location (bp) | Effect allele | Breast cancer GWAS results | Conditional analysis, LD from 1000 G phase 3 (EUR) | ||
|---|---|---|---|---|---|---|---|---|---|---|
Frequency | β | PGWAS | Pconda | |||||||
cg14494596 | 3 | 48542040 | 3q21.31 | rs34071734 | 49425004 | A | 0.061 | −0.042 | 1.56 × 10−3 | – |
rs767512 | 48023924 | C | 0.290 | −0.018 | 9.24 × 10−3 | 4.95 × 10−3 | ||||
rs13095891 | 48381826 | T | 0.053 | −0.036 | 1.15 × 10−2 | 5.93 × 10−3 | ||||
rs112445131 | 47786930 | T | 0.175 | −0.012 | 1.51 × 10−1 | 4.59 × 10−3 | ||||
rs3895736 | 48658467 | A | 0.172 | −0.013 | 1.20 × 10−1 | 1.70 × 10−3 | ||||
rs73078357 | 48695834 | C | 0.126 | −0.014 | 1.45 × 10−1 | 1.36 × 10−2 | ||||
cg03958883 | 11 | 73020729 | 11q13.4 | rs11235743 | 73124826 | G | 0.216 | 0.023 | 2.59 × 10−3 | – |
rs11602616 | 72364077 | C | 0.166 | 0.025 | 4.34 × 10−3 | 7.24 × 10−3 | ||||
rs7116276 | 72276606 | T | 0.315 | 0.013 | 5.76 × 10−2 | 1.68 × 10−2 | ||||
rs77383504 | 72265531 | G | 0.055 | 0.024 | 1.13 × 10−1 | 1.95 × 10−2 | ||||
rs11235541 | 72285444 | A | 0.046 | 0.017 | 3.12 × 10−1 | 4.50 × 10−2 | ||||
rs61893925 | 72274449 | T | 0.111 | 0.019 | 5.88 × 10−2 | 3.59 × 10−2 | ||||
cg16555866 | 17 | 80830922 | 17p11.2 | rs78483419 | 80870884 | C | 0.180 | −0.032 | 7.78 × 10−5 | – |
rs8076573 | 80496771 | G | 0.712 | 0.025 | 1.62 × 10−3 | 4.98 × 10−4 | ||||
rs78165269 | 80601498 | C | 0.304 | −0.024 | 8.72 × 10−4 | 2.79 × 10−3 | ||||
rs4789841 | 80739952 | T | 0.073 | −0.024 | 6.73 × 10−2 | 1.07 × 10−2 | ||||
