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Table 2 List of regSNVs associated with the expression of their target genes in TCGA primary tumors

From: Non-coding single nucleotide variants affecting estrogen receptor binding and activity

RegSNV ID Location Target gene No. of tumors with SNV genotype (n = 501) log2 fold change Adjusted p value
rs36208869 Promoter GSTM1 32 4.58 1.25E-08
rs1131017 Promoter RPS26 318 –0.39 5.19E-07
rs7113753 Promoter TRAPPC4 180 0.26 2.79E-05
rs1412825 Promoter LRRIQ3 243 –0.22 3.64E-05
rs34282253 Promoter XKR9 119 0.41 4.62E-05
rs10747783 Promoter TSFM 205 –0.22 0.000157917
rs252923 Promoter SETD9 197 0.41 0.000157917
rs41293275 Promoter NSUN4 175 –0.22 0.000241865
rs3213745 Promoter CEBPZ 241 –0.19 0.000444457
rs2732649 intergenic LRRC37A 132 0.12 0.002214471
rs17361749 Promoter NSUN4 168 –0.2 0.002736821
rs10489769 Promoter NSUN4 172 –0.19 0.004515197
rs10956142 intergenic ANXA13 38 –0.29 0.004515197
rs2939587 Promoter TM2D3 260 0.21 0.005471564
rs1291363 Promoter HTR7P1 315 0.59 0.006560413
rs4418583 Intron LDLRAP1 248 0.24 0.006560413
rs3811254 Intron OR4E2 3 0.04 0.009385423
  1. The tumors containing regSNVs were identified using SNP genotyping and the expression of target genes were compared between WT and variant carriers. This table shows the top regSNVs significantly regulating their corresponding target genes (adjusted p value < 0.01)