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.