Table 4. The information of selected 39 SNPs in ERCC2, PPP1R13L, CD3EAP and ERCC1 on Chr19q13.3.
| Gene/dbSNP ID | Location | Position | Base change | Allele frequency in HapMap CHB | MAF in control group | Genotyping technique |
|---|---|---|---|---|---|---|
| ERCC2a | ||||||
| rs238418 | intron | 45855262 | C/T | C0.675/A0.325 | A0.33 | Sequenom |
| rs1799787/Tag | intron | 45856144 | C/T | C0.932/T0.068 | T0.06 | PCR-RFLP |
| rs3916874/Tag | intron | 45856926 | G/C | G0.811/C0.189 | C0.17 | PCR-RFLP |
| rs238415/Tag | intron | 45857235 | C/G | C0.525/G0.475 | G0.45 | Sequenom |
| rs238414 | intron | 45857820 | C/T | C0.608/T0.392b | T0.48 | Sequenom |
| rs2070831 | intron | 45858246 | C/T | C0.767/T0.233b | T 0.27 | Sequenom |
| rs3916840/Tag | intron | 45862297 | C/T | C0.944/T0.056 | T 0.04 | PCR-RFLP |
| rs50872/Tag | intron | 45862449 | C/T | C0.709/T0.291 | T0.19 | Sequenom |
| rs50871/Tag | intron | 45862515 | T/G | T0.678/G0.322 | G0.25 | Tag-Man |
| rs238403/Tag | intron11 | 45865217 | C/T | C0.560/T0.440 | T0.47 | PCR-RFLP |
| rs2097215c | 5′ near gene | 45875787 | A/G | A0.537G0.463 | G0.49 | Sequenom |
| PPP1R13L a | ||||||
| rs6966/Tag | 3′ UTR | 45882962 | A/T | A0.500/T0.500 | T0.48 | PCR-RFLP |
| rs8112723c | intron | 45885279 | A/T | A0.533/T0.467b | T0.31 | Sequenom |
| rs201704c | intron | 45887265 | A/T | No | T0.49 | Sequenom |
| rs2070830/Tag | intron | 45889650 | G/T | G0.667/T0.333 | T0.28 | Sequenom |
| rs1970764 | intron8 | 45890873 | A/G | No | G0.46 | LDR-PCR |
| rs10418623d | intron | 45891670 | G/A | G0.667/A0.333b | 0 | Sequenom |
| rs35209357 | intron | 45892719 | G/C | G0.692/C0.308b | C0.3 | Sequenom |
| rs34231843 | intron8 | 45893623 | A/G | A0.692/G0.308b | G0.29 | Sequenom |
| rs4802252/Tag | intron | 45904759 | C/T | C0.732/T0.268b | T0.24 | LDR-PCR |
| rs4803816 | intron | 45904888 | T/C | T0.707/C0.293 | C0.24 | Sequenom |
| rs4803817/Tag | intron1 | 45907960 | A/G | A0.678/G 0.322 | G0.34 | LDR-PCR |
| rs1005165 | 5′ near gene | 45909050 | C/T | C0.575/T0.425 | T0.43 | Sequenom |
| CD3EAP a | ||||||
| rs967591 | 5′ UTR | 45909934 | G/A | G0.525/A0.475b | A0.39 | LDR-PCR |
| rs8113779 | intron | 45910003 | G/T | G0.517/T0.483b | T0.43 | Sequenom |
| rs1046282/Tag | intron/3′ UTR for ERCC1 | 45910672 | T/C | T0.673/C0.327b | C0.34 | LDR-PCR |
| rs735482/Tag | exon3/3′ UTR for ERCC1 | 45912002 | A/C | A0.556/C0.444 | C0.44 | LDR-PCR |
| rs3212986c | exon3/3′ UTR for ERCC1 | 45912736 | G/T | G0.686/T0.314 | T0.33 | Sequenom |
| rs1007616 | 3′ UTR | 45913093 | C/T | C0.683/T0.317b | T0.25 | Sequenom |
| rs62109563 | 3′ near gene | 45914046 | T/C | T0.650/C 0.350b | C0.35 | Sequenom |
| ERCC1 a | ||||||
| rs3212980/Tag | intron | A/C | A0.679/C0.321b | C0.34 | LDR-PCR | |
| rs3212967d | intron | 45920264 | C/T | C0.550/T0.450b | T1.0 | Sequenom |
| rs3212965 | intron5 | 45920580 | C/T | C0.689 /T0.311 | T0.33 | Sequenom |
| rs3212964/Tag | intron5 | 45920796 | G/A | G0.567/A0.433 | A0.43 | LDR-PCR |
| rs3212961/Tag | intron | 45922323 | A/C | A0.500/C0.500 | A0.48 | LDR-PCR |
| rs3212955 | intron | 45923496 | A/G | A0.711/G0.289 | G0.29 | Sequenom |
| rs11615/Tag | exon4 | 45923653 | G/A | G0.778/A0.222 | A0.23 | PCR-RFLP |
| rs3212950d | intron | 45924086 | C/G | C0.658/G0.342b | C1.0 | Sequenom |
| rs2298881/Tag | intron | 45926916 | T/C | T0.517/A0.444 | A0.4 | LDR-PCR |
a
The information from NCBI SNP database (37.3 Genome Build) and HapMap database
b
CHB+JPT
c
Hardy-Weinberg equilibrium departure
d
Genotyping fail