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Table 2 Functional annotation of the identified EMSY SNPs with rs IDs

From: Germline EMSY sequence alterations in hereditary breast cancer and ovarian cancer families

SNP

Location

Conserved region

Open chromatina;

Regulatory chromatin statea;

Protein binding

Motifs changed

GERP

SiPhy

Cell IDb

(Cell IDb)

rs4245443

intron

No

No

Pou1f1_2, YY1_known6

rs2508740

intron

No

Yes

rs11600501

intron

Yes

Yes

7_Weak_Enhancer (HepG2)

EWSR1-FLI1, GATA_known8,

TATA_disc7

rs11363199

intron

No

No

7_Weak_Enhancer (HepG2)

Foxa_known4, Pou1f1_2,

Pou2f2_known2, Pou3f2_2, Sox_5

rs184345272

exon

Yes

Yes

NRSF_known3

rs3753051

exon

Yes

Yes

HeLa-S3

CEBPB_disc2, Foxa_known2

rs2513513

3′UTR

Yes

Yes

HA-sp., HCPEpiC,

5_Strong_Enhancer (Huvec)

HMVEC-dBl-Neo

rs148932730

3′UTR

Yes

Yes

4_Strong_Enhancer (Huvec)

DMRT2, Nanog_disc2, Sox_13,

Sox_14, Sox_16, Sox_18, Sox_19,

Sox_2, Sox_4, Sox_9

rs187735484

3′UTR

Yes

No

HMVEC-LBl,

4_Strong_Enhancer (Huvec)

TATA_disc7

HMVEC-dLy-Neo

rs72932407

3′UTR

Yes

No

HBMEC, HMVEC-LBl,

4_Strong_Enhancer (Huvec)

MAZ, SREBP_known3

HMVEC-dLy-Neo,

HPAEC, HRGEC

rs1044265

3′UTR

Yes

Yes

HUVEC

5_Strong_Enhancer (Huvec)

Foxo_3, Mef2_known1, Mef2_known6,

Pou2f2_known2, TCF4_known3

  1. aThe ENCODE data [40]
  2. b HeLa-S3 cervical carcinoma, HA-sp. astrocytes spinal cord, HCPEpiC choroid plexus epithelial cells, HMVEC-dBl-Neo neonatal blood microvascular endothelial cells, dermal-derived, HMVEC-LBl blood microvascular endothelial cells, lung-derived, HMVEC-dLy-Neo neonatal lymphatic microvascular endothelial cells, dermal-derived, HBMEC brain microvascular endothelial cells, HPAEC pulmonary artery endothelial cells, HRGEC renal glomerular endothelial cells, HUVEC umbilical vein endothelial cells, HepG2 hepatocellular carcinoma