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Table 7 Top intronic SNVs in breast

From: Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA

Gene

dbSNP ID

Locus (Chr:bp)

Variant

Class

Description

HFM1

NA

1:91852851

A →G

ER+

A DNA helicase that is specifically expressed in germline cells [75]

EML4

rs7233

2:42396722

A →G

TR-

EML4-ALK mutants are frequently found in NSCLC and some breast cancers [69]

ARHGEF16

rs4534324

1:3394674

T →C

ER+

Promotes migration and invasion of breast cancer cells [29]

LRRC56

rs7396875

11:551405

G →A

ER+

Uncharacterized in humans [68]

LMNTD2

rs936466

11:557342

T →C

ER+

Uncharacterized lamnin tail containing domain protein [68]

CTBP1

rs1250100

4:1236182

A →G

ER+

Downregulates BRCA and E-cadherin in breast cancer, potential biomarker for cancer development [23]

HDAC7

rs3815138

12:48178465

T →C

ER+

Promotes breast cancer cell survival and therapy resistance by inhibiting autophagic cell death [80]

SNED1

rs6715941

2:241993027

C →T

ER+

High expression is correlated with poor outcome for ER-/PR- breast cancer patients [61]

CTBP2

rs4962716

10:126685867

T →C

ER+

High expression is associated with E-cadherin and cellular proliferation in breast cancer [53]

CD151

rs28454516

11:833828

G →A

ER+

Deregulation is predictive of poor outcome in node-negative lobular breast carcinoma [70]

DLG2

rs4943920

11:85195154

A →T

TR-

The location of DLG2 is a common fragile site and is under expressed in several cancers [57]

ARHGEF16

rs4422946

1:3394640

A →G

ER+

Promotes migration and invasion of breast cancer cells [29]

OAZ1

rs2523174

19:2271181

T →C

ER+

mRNA biomarker for oral cancer patients [20]

GAA

rs12944802

17:78084418

G →A

ER+

Acid alpha-glucosidase, which is essential for the degradation of glycogen to glucose in lysosomes [68]

HDAC7

rs3815132

12:48179048

C →T

ER+

Promotes breast cancer cell survival and therapy resistance by inhibiting autophagic cell death [80]