Skip to main content

Table 1 Characteristics of SNPs analyzed

From: Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes

Gene

SNP Code

SNP ID

Base change*

Position†

MAF‡

ABI reported MAF§

# bp from the most 5' SNP

ATM

A1

rs228589

T/A

Flanking

0.45

0.33

0

ATM

A2

rs228591

G/A

mRNA-utr

0.45

0.33

4125

ATM

A3

rs641605

T/C

Intron

0.45

0.33

8,711

ATM

A4

rs228599

A/G

Intron

0.44

0.31

14,452

ATM

A5

rs600931

T/C

Intron

0.45

0.35

24,127

ATM

A6

rs228592

A/C

Intron

0.45

0.33

29,981

ATM

A7

rs664677

T/C

Intron

0.43

0.33

49,974

ATM

A8

rs1003623

T/C

Intron

0.45

0.33

59,374

ATM

A9

rs609261

C/T

mRNA-utr, intron

0.45

0.32

64,926

ATM

A10

rs645485

G/A

Intron

0.45

0.32

75,655

ATM

A11

rs673281

A/G

Intron

0.45

0.31

88,861

ATM

A12

rs227061

G/A

mRNA-utr, intron

0.45

0.34

112,121

ATM

A13

rs227062

A/G

mRNA-utr, intron

0.45

0.33

112,175

ATM

A14

rs652311

A/G

Flanking

0.45

0.36

146,861

MRE11

M1

rs646130

T/C

Flanking

0.3

0.39

0

MRE11

M2

rs491404

G/C

Flanking

0.3

0.4

9192

MRE11

M3

rs10831227

G/A

Intron

0.3

0.4

16,336

MRE11

M4

rs601341

G/A

Intron

0.38

0.36

28,536

MRE11

M5

rs554715

T/C

Intron

0.3

0.4

32,986

MRE11

M6

rs556477

A/G

Intron

0.3

0.4

40,565

MRE11

M7

rs1805365

A/G

Intron

0.02

0.02

61,721

MRE11

M8

rs680695

A/G

Intron

0.34

0.36

72,913

MRE11

M9

rs1009455

C/G

Intron

0.02

0.01||

85,033

MRE11

M10

rs1009456

C/A

locus-region, mRNA-utr

0.01

0.02

87,401

MRE11

M11

rs10831234

C/T

Flanking

0.09

0.06

93,946

NBS1

N1

rs12680687

G/T

Intron

- **

0.28

0

NBS1

N2

rs709816

A/G

Coding-synon

-

0.45

16,323

NBS1

N3

rs1805790

C/T

Intron

-

0.39

23,313

NBS1

N4

rs741778

C/G

Intron

-

0.36

33,415

NBS1

N5

rs1805841

C/G

Intron

-

0.45

41,282

RAD50

R1

rs2522406

G/A

Flanking

-

0.01

0

RAD50

R2

rs2244012

C/T

Intron

-

0.19

12,116

RAD50

R3

rs2299015

T/G

Intron

-

0.19

12,388

RAD50

R4

rs2299014

G/T

Intron

-

0.41

14,290

RAD50

R5

rs2706377

A/G

Intron

-

0.01

50,388

RAD50

R6

rs2301713

C/T

intron

-

0.19

62,887

RAD50

R7

rs2040703

C/G

Intron

-

0.22

83,149

RAD50

R8

rs2240032

C/T

Intron

-

0.18

88,018

RAD50

R9

rs1800925

C/T

Flanking

-

0.19

103,700

RAD50

R10

rs2066960

C/A

Flanking

-

0.17

105,326

XRCC4

X1

rs1993948

T/A

Flanking

0.46

0.47

0

XRCC4

X2

rs1478485

G/A

mRNA-utr

0.47

0.45

8247

XRCC4

X3

rs11951257

T/C

Intron

0.47

0.45

31,031

XRCC4

X4

rs10045104

C/T

Intron

0.43

0.42

40,082

XRCC4

X5

rs6452526

C/T

Intron

0.47

0.43

64,531

XRCC4

X6

rs1382369

G/A

Intron

0.47

0.43

69,149

XRCC4

X7

rs1382368

C/T

Intron

0.47

0.41

78,795

XRCC4

X8

rs1382363

C/T

Intron

0.47

0.42

80,292

XRCC4

X9

rs13180316

G/A

Intron

0.23

0.26

87,173

XRCC4

X10

rs11741420

A/T

Intron

0.47

0.44

98,452

XRCC4

X11

rs2731861

T/C

Intron

0.47

0.45

112,984

XRCC4

X12

rs2662238

G/A

Intron

0.46

0.45

127,027

XRCC4

X13

rs1039786

C/T

Intron

0.46

0.45

127,761

XRCC4

X14

rs963248

T/C

Intron

0.19

0.16

161,614

XRCC4

X15

rs301276

G/A

Intron

0.23

0.23

175,451

XRCC4

X16

rs35268

T/C

Intron

0.16

0.13

216,216

XRCC4

X17

rs301286

T/C

Intron

0.16

0.18

230,675

XRCC4

X18

rs301289

C/T

Intron

0.17

0.17

233,955

XRCC4

X19

rs2386275

G/A

Intron

0.09

0.12

270,260

XRCC4

X20

rs2891980

T/C

Intron

0.09

0.13

270,383

XRCC4

X21

rs1056503

T/G

Coding-synon

0.09

0.12

276,697

  1. * Base change listed as Major allele / Minor allele
  2. † Position obtained from the University of California, Santa Cruz Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway; Flanking = within 10 kb of either side of gene; Locus region = variation in region of gene, but not in transcript; mRNA-utr = variation in transcript, but not in coding region interval
  3. ‡ MAF = minor allele frequency using our panel of 94 breast cancer case and control subjects
  4. §Applied Biosystems reported minor allele frequency in Caucasians
  5. || Corrected value. Applied Biosystems acknowledged error in reported minor allele frequency of 0.49 on their web site, but it has not been updated.
  6. ** NBS1 and RAD50 were not genotyped in the current study. All analyses for these two genes were performed using the raw genotype data freely available online from Applied Biosystems. Base change obtained from University of California, Santa Cruz Genome Browser.
Back to article page

BMC Cancer

ISSN: 1471-2407

Contact us