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Table 1 The polymorphisms used in this study, their kind and their identification

From: Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP

New trivial name1

Systematic name2

Series3

rs#4

contig pos5

relativ position6

XPD-exon23

ERCC2 c.2282A>C

L1

13181

18123137

0

XPD-exon10

ERCC2 c.965G>A

L1

1799793

18135477

12340

XPD-exon6

ERCC2 c.499A>C

L1 + S

238406

18136527

13390

XPD-intron5-1

ERCC2 c.492-62T>A

S

238407

18136696

13559

XPD-intron5-2

ERCC2 c492-892A>G

S

3916809

18137426

14289

XPD-intron5-3

ERCC2 c.391+311A>G

S

 

18139824

16687

XPD-intron3-1

ERCC2 c.278-35G>A

L1

1799783

18140254

17117

XPD-5'1

ERCC2 c.-35-113G>C

S

3810366

18142160

19023

XPD-5'd1

ERCC2 c.-35-298_-294delGACA

L1 + S

3916791

18142345

19208

XPD-5'4

ERCC2 c.-35-583A>C

L2

3916788

18142630

19493

XPD-5'd2

ERCC2 c.-35-980_-979ins80

A

3916787

18143027

19890

XPD-5'2

ERCC2 c.-35-1958A>G

L1 + S

2097215

18144005

20868

XPD-5'3

g.18145185T>C

L1 + S

11878644

18145185

22048

RAI-3'd2

g. 18145752_18145773del(22)

A

 

18145768

22631

RAI-3'8

g.18142233C>A

S

 

18146233

23096

RAI-3'7

g.18146823C>T

L1

7252567

18146823

23686

RAI-3'd1

g.18147012ATTTT(2_11)

A

7255792

18147012

23875

RAI-3'9

g.18147126T>C

L2

2377329

18147126

23989

RAI-3'd3

g.18147199delTT

A

3047560

18147192

24055

RAI-3'10

g.18147886T>G

S + L2

10422489

18147886

24749

RAI-3'11

g.18148193C>T

L2

10426701

18148193

25056

RAI-3'4

g.18150199A>G

L1 + S

4544343

18150199

27062

RAI-exon 13-2

PPP1R13L c.*507T>G

S

 

18151158

28021

RAI-exon13-1

PPP1R13L c.*475T>A

T + S

6966

18151180

28043

RAI-intron12-1

PPP1R13L c.2515-68G>A

S

 

18151772

28635

RAI-intron12-4

PPP1R13L c.2515-330G>C

S

 

18152034

28897

RAI-intron12-3

PPP1R13L c.2515-467G>A

L1

10417235

18152171

29034

RAI-intron12-5

PPP1R13Lc.2515-1150G>A

L2

12876252

18152764

29627

RAI-intron12-2

PPP1R13L c.2514+505T>A

L1

8112723

18153497

30360

RAI-intron11-2

PPP1R13L c.2315-594T>G

S

 

18154796

31659

RAI-intron11-1

PPP1R13L c.2315-1281G>A

L1 + S

2017104

18155483

32346

RAI-intron11-2

PPP1R13L c.2248+1167G>T

S

 

18155871

32734

RAI-intron8-1

PPP1R13L c.1882-1425A>G

L1

1970764

18159091

35954

RAI-intron8-10

PPP1R13L c.1882-1263A>G

S

 

18159263

36126

RAI-intron8-9

PPP1R13L c.1882-1697A>G

L2

 

18160363

37226

RAI-intron8-4

PPP1R13L c.1882-2270T>G

S

 

18160936

37799

RAI-intron8-5

PPP1R13L c.1882-2271G>C

S

 

18160937

37800

RAI-intron8-11

PPP1R13l c.1881+1912G>T

S

 

18161433

38296

RAI-intron8-6

PPP1R13L c.1881+1514A>G

S

 

18161841

38704

RAI-intron8-2

PPP1R13L c. 1881+1149B>A

L1

6509210

18162206

39069

RAI-intron8-12

PPP1R13l c.1881+756C>T

L2

12986272

18162599

39462

RAI-intron8-7

PPP1R13L c 1881+452T>G

S

 

18162903

39766

RAI-intron8-8

PPP1R13L c.1881+389T>C

S

 

18162986

39849

RAI-intron8-3

PPP1R13L c.1881+385T>G

L1

 

18162970

39833

RAI-intron7-1

PPP1R13L c.1421-1236G>C

S

 

18165052

41915

RAI-intron3-2

PPP1R13L c.264-404G>A

L1

4803814

18168944

45807

RAI-intron3-3

PPP1R13L c.264-408G>A

L1

4803815

18168948

45811

RAI-intron1-5

PPP1R13L c.-21-1304insTAAG

S

 

18171119

47982

RAI-intron1-7

PPP1R13L c.-21-1931G>T

S

10402584

18171746

48609

RAI-intron1-10

PPP1R13Lc.-21-2062G>A

S

10401293

18171815

48678

RAI-intron1-1

PPP1R13L c.-21-2169A>G

L1 + S

4572514

18171984

48847

RAI-intron1-4

PPP1R13L c.-21-3291G>A

L2 + S

4803816

18173106

49969

RAI-intron1-8

PPP1R13L c.-21-3291A>G

S

 

18173107

49970

RAI-intron1-2

PPP1R13L c.-22+1148C>T

L1

2226949

18175327

52190

RAI-intron1-3

PPP1R13L c.-22+734A>G

L2

959457

18175739

52602

RAI-intron1-9

PPP1R13L c.-22+379T>C

S

 

18176096

52959

RAI-intron1-5

PPP1R13L c.-22+297T>C

L2 + S

4803817

18176178

53041

RAI-5'1

PPP1R13L c-54-177T>C

L1 + S

10412761

18176680

53543

ASE1-exon1

CD3EAP c.-468-21G>A

L1

967591

18178152

55015

ASE1-exon2

CD3EAP c.22+29A>C

S

 

18178222

55085

ASE1-exon3-4

CD3EAP c.564G>C

S

 

18178623

55486

ASE1-exon3-1

CD3EAP c.1264A>G

T

735482

18180220

57083

ASE1-exon3-2

CD3EAP c.1605A>G

L1 + S

762562

18180561

57424

ASE1-exon3-3

CD3EAP c.1668G>A

T + S

2336219

18180624

57487

ASE1-exon3-d1

CD3EAP c.1751TTC(5_6)

A

3212987

18180707

57570

ASE1-exon3-6

CD3EAP c.1998C>A

L1 + S

3212986

18180954

57817

ASE1-exon3-4

CD3EAP c.*1228T>C

L2

3212983

18182205

59068

ERCC1-exon4

ERCC1 c.500T>C

L1

11615

18191871

68734

  1. 1) The trivial names have been changed to conform to the new model of the RAI gene, which involves a major 5' extension of the gene relative to older models. Specifically, the polymorphism previously called RAI intron1 is now called RAI-intron8-1. Similarly RAI exon6 is now called RAI-exon13-1.
  2. 2) The systematic name according to http://www.hgvs.org/mutnomen/recs.html
  3. 3) The series of assays to which the polymorphism belongs
  4. L1: First series of Lightcycler assays
  5. L2: Later series of Lightcycler assays
  6. A: Assays on ABI3100
  7. T: Assays on Taqman
  8. S: Assays on Sequenom
  9. 4) The rs-number of the polymorphisms in NCBI's database dbSNP
  10. 5) Positions of the polymorphisms in the contig [GenBank: NT_011109.15]
  11. 6) Positions of the polymorphisms relative to XPD-exon23
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BMC Medical Genetics

ISSN: 1471-2350

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