Table 1.
Characteristics of SNPs analyzed
| 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 |
* Base change listed as Major allele / Minor allele
† 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
‡ MAF = minor allele frequency using our panel of 94 breast cancer case and control subjects
§Applied Biosystems reported minor allele frequency in Caucasians
|| Corrected value. Applied Biosystems acknowledged error in reported minor allele frequency of 0.49 on their web site, but it has not been updated.
** 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.