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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