Table 1 Characteristics and functional prediction of the core NER genes and their regulatory region SNPs.

From: Genetic variants in ERCC1 and XPC predict survival outcome of non-small cell lung cancer patients treated with platinum-based therapy

Gene

SNP ID

Chr.

Position

Gene ___location

Allelesa

TFBSb

Splicingc

miRNA

MAFd

Detected MAF

eQTLe

Call rate

HWE

Tagging SNPs

ERCC1

rs3212986

19

45409478

3′UTR

C > A

—

—

—

0.31

0.34

Y

99.9%

0.350

4

 

rs2298881

19

45423658

Intron

C > A

Y

—

—

0.43

0.3

Y

93.0%

0.028

0

 

rs3212924

19

45425445

5′ near gene

A > G

Y

—

—

0.28

0.31

Y

99.7%

0.868

0

 

rs3212930

19

45424352

5′UTR

A > G

Y

—

—

0.12

0.1

Y

95.9%

0.894

0

ERCC2/XPD

rs50871

19

45359257

Intron

A > C

—

—

—

0.27

0.29

N

99.9%

0.081

0

 

rs3916788

19

45371154

5′UTR

C > A

Y

—

—

0.51

0.48

Y

97.2%

0.159

0

 

rs238416

19

45353791

Intron

C > T

—

—

—

0.47

0.47

Y

99.9%

0.010

4

 

rs2097215

19

45372529

5′near gene

C > T

Y

—

—

0.49

0.5

Y

99.9%

0.066

12

ERCC3/XPB

rs4150477

2

127274970

Intron

A > G

—

—

—

0.45

0.41

Y

99.9%

0.001

26

 

rs13385611

2

127247114

5′ near gene

T > C

Y

—

—

0.12

0.12

N

99.7%

0.437

17

 

rs3738948

2

127260487

Intron

A > G

—

—

—

0.33

0.29

Y

99.6%

0.094

19

ERCC4/XPF

rs1799798

16

13920421

Intron

G > A

Y

—

—

0.15

0.12

N

100.0%

0.307

0

 

rs3136038

16

13919522

5′ near gene

C > T

Y

—

—

0.22

0.23

Y

99.9%

0.317

42

ERCC5/XPG

rs751402

13

102845848

5′UTR

G > A

Y

Y

—

0.35

0.36

Y

99.9%

0.233

11

 

rs2094258

13

102844409

Intron

C > T

Y

—

—

0.36

0.37

N

99.9%

0.151

9

 

rs3759497

13

102844227

Intron

G > A

Y

—

—

0.37

0.4

Y

99.9%

0.043

0

 

rs2296147

13

102846025

5′UTR

T > C

Y

—

—

0.23

0.21

Y

99.9%

0.981

10

 

rs873601

13

102875987

3′UTR

A > G

—

Y

Y

0.48

0.5

N

100.0%

0.822

5

XPC

rs1982546

3

14175789

Intron

C > A

Y

—

—

0.25

0.26

N

99.6%

0.680

17

 

rs2229090

3

14145845

3′UTR

G > C

—

—

Y

0.33

0.36

N

99.9%

0.797

6

 

rs2607772

3

14177502

Intron

G > A

Y

—

—

0.38

0.37

N

99.9%

0.018

12

 

rs2607775

3

14178595

5′UTR

C > G

Y

Y

—

0.05

0.04

Y

98.2%

0.297

19

XPA

rs1800975

9

97697296

5′UTR

T > C

Y

Y

—

0.48

0.46

Y

100.0%

0.963

13

 

rs3176623

9

97698702

5′ near gene

C > A

Y

—

—

0.10

0.14

N

99.7%

0.178

0

RAD23B

rs7041137

9

107282291

Upstream

C > T

Y

—

—

0.17

0.22

N

99.9%

0.785

48

DDB1/XPE

none

             
  1. aMajor > Minor allele; bTranscription factor binding site; cEnhance or abolish ___domain; dMinor allele frequency in Chinese Han Beijing (CHB); eExpression quantitative trait loci
  2. Abbreviations: SNP, single nucleotide polymorphism; Chr, chromosome; MAF, minor allele frequency; eQTL, expression quantitative trait loci; HWE, Hardy-Weinberg equilibrium; UTR, untranslated region; NER, nucleotide excision repair.
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