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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)