Table 2 SNPs with significant differential imprinting in control samples versus breast cancer and the different subtypesa

From: A comprehensive overview of genomic imprinting in breast and its deregulation in cancer

SNP Gene Tumour HER2-enriched Basal-like Luminal A Luminal B
   DI_p logFC DE_p DI_p logFC DE_p DI_p logFC DE_p DI_p logFC DE_p DI_p logFC DE_p
rs1053900 MEG3 0.49 −2.4 6.6E-45 0.07 −2.2 5.6E-18 1.00 −3.0 1.8E-37 0.90 −2.2 1.6E-29 0.46 −2.7 1.1E-35
rs4378559 MEG3 0.49 −1.7 2.8E-27 0.04 −1.0 2.0E-08 1.00 −2.4 6.8E-26 0.92 −1.4 1.6E-16 0.46 −2.2 2.2E-26
rs12890215 MEG3 0.47 −1.7 5.1E-29 0.10 −1.0 5.7E-09 0.76 −2.3 8.0E-27 0.87 −1.4 9.1E-18 0.44 −2.2 6.7E-28
rs10863 MEST 0.02 −1.6 1.3E-31 0.00 −1.7 3.0E-13 0.70 −0.9 6.5E-15 0.03 −1.9 5.4E-31 0.00 −1.7 2.7E-19
rs3741219 H19 0.17 −0.9 1.4E-02 0.00 −1.1 1.4E-03 0.03 −0.8 4.5E-04 0.77 −0.7 3.5E-01 0.38 −1.3 7.8E-04
rs2839704 H19 0.07 −0.9 2.1E-02 0.01 −1.2 8.1E-04 0.02 −0.8 9.7E-04 0.40 −0.7 4.5E-01 0.03 −1.2 8.3E-04
rs2839703 H19 0.08 −0.9 2.7E-02 0.01 −1.3 9.8E-04 0.02 −0.8 1.4E-03 0.56 −0.8 4.7E-01 0.03 −1.3 9.8E-04
rs10840159 H19 0.17 −1.0 3.4E-02 0.01 −1.4 2.3E-03 0.02 −0.9 1.3E-03 0.85 −0.8 4.8E-01 0.27 −1.3 1.3E-03
rs2839702 H19 0.17 −0.7 3.3E-02 0.01 −1.0 7.0E-03 0.02 −0.5 4.9E-04 0.65 −0.5 4.1E-01 0.16 −1.0 4.2E-03
rs2839701 H19 0.17 −0.6 6.4E-02 0.01 −0.9 9.5E-03 0.03 −0.5 1.1E-03 0.76 −0.5 4.9E-01 0.22 −0.9 8.7E-03
rs2067051 H19 0.19 −0.3 4.8E-01 0.05 −0.6 4.8E-01 0.02 −0.2 1.1E-01 0.91 0.0 4.7E-03 0.20 −0.6 1.9E-01
rs2075745 H19 0.17 −0.4 8.6E-01 0.04 −0.8 3.3E-01 0.02 −0.4 6.1E-02 0.78 −0.2 2.6E-02 0.16 −0.7 1.4E-01
rs2075744 H19 0.27 −0.2 4.1E-01 0.17 −0.6 2.8E-01 0.02 −0.3 1.9E-01 0.92 0.0 1.7E-02 0.57 −0.4 3.6E-01
rs2839698 H19 0.23 −0.3 4.5E-01 0.08 −0.7 3.8E-01 0.02 −0.4 1.4E-01 0.90 −0.1 1.4E-02 0.38 −0.5 3.7E-01
rs7582864 ZDBF2 0.49 −1.7 2.7E-25 0.75 −2.8 1.1E-21 0.10 −1.5 8.5E-14 0.87 −1.6 2.1E-18 0.75 −1.4 7.1E-16
rs3732084 ZDBF2 0.17 −1.6 1.2E-28 0.14 −2.3 1.9E-19 0.02 −1.5 5.7E-17 0.53 −1.6 2.0E-21 0.46 −1.5 3.8E-19
rs1975597 ZDBF2 0.27 −1.5 3.6E-29 0.08 −2.2 4.0E-19 0.15 −1.5 9.9E-17 0.52 −1.4 5.4E-22 0.57 −1.3 1.2E-19
rs2585 IGF2 0.17 −1.1 5.9E-33 0.02 −2.3 3.0E-22 0.08 0.2 1.3E-35 0.44 −1.3 7.3E-15 0.10 −2.3 6.1E-29
rs7873 IGF2 0.43 −1.2 2.9E-33 0.14 −2.4 3.9E-22 0.03 0.1 5.3E-36 0.78 −1.4 2.1E-15 0.92 −2.3 1.8E-28
rs6059869 HM13 0.17 0.3 8.3E-02 0.10 0.0 3.8E-01 0.13 0.2 4.0E-01 0.68 0.3 3.1E-02 0.03 0.6 7.2E-03
rs6059873 HM13 0.06 0.4 3.2E-03 0.02 0.2 2.8E-01 0.02 0.4 9.1E-02 0.33 0.4 1.5E-03 0.02 0.6 5.6E-04
rs8110538 ZNF331 0.27 −0.9 3.2E-25 0.63 −1.1 9.1E-18 0.08 −1.0 4.5E-16 0.75 −0.9 4.3E-19 0.08 −0.8 3.3E-15
rs8110350 ZNF331 0.30 −0.9 3.5E-25 0.44 −1.0 5.8E-18 0.08 −1.0 1.0E-15 0.81 −0.9 1.4E-19 0.10 −0.7 2.1E-14
rs7810469 PEG10 0.19 1.0 8.3E-03 0.04 0.9 1.2E-01 0.58 1.2 1.2E-01 0.53 1.0 2.8E-04 0.10 0.9 8.3E-04
  1. aFDR-adjusted p-values are listed in column DI_p with significant results (FDR ≤ 0.1) shown in bold. Also log-fold changes (logFC) and FDR adjusted p-values of differential expression analysis (DE_p) are listed with significant results (FDR ≤ 0.05) shown in bold