Table 1.
SNP functional consequences
| Panel A: as reported in previous studies | ||||
|---|---|---|---|---|
| dbSNP | Chrom | Gene | Functional consequences | |
| rs293794 | 3 | hOGG1 | I | |
| rs1052133 | 3 | hOGG1 | 3′ UTR, NS (S326C) | |
| rs3136820 | 14 | APEX1 | NS (D148E) | |
| rs2272615 | 8 | POLB | I | |
| rs2953993 | 8 | POLB | I | |
| rs1799782 | 19 | XRCC1 | NS (R194W) | |
| rs25487 | 19 | XRCC1 | NS (Q399R) | |
| rs2248690 | 3 | AHSG | Promoter | |
| rs4918 | 3 | AHSG | Thr/Ser | |
| rs1071592 | 3 | AHSG | Thr/Thr | |
| Panel B: computed using SNPnexus | ||||
|---|---|---|---|---|
| dbSNP | Gene | Source | Transcripts | Functional consequences [peptide shift (if any), number of transcripts] |
| rs293794 | hOGG1 | RefSeq | 5 | |
| Ensembl | 6 | |||
| VEGA | 6 | I | ||
| UCSC | 5 | |||
| AceView | 8 | |||
| CAMK1 | RefSeq | 1 | I (1) | |
| Ensembl | 2 | I (2) | ||
| VEGA | 2 | I (2) | ||
| UCSC | 3 | I (2); 5up (1) | ||
| AceView | 6 | I (4); 5up (1); 5′UTR (1) | ||
| rs1052133 | hOGG1 | RefSeq | 8 | NS (S326C, P332A, 2); 3′UTR (1); I (5) |
| Ensembl | 11 | NS (S326C, P119A, P332A, 3); 3′UTR (1); I (6); 3down (1) | ||
| VEGA | 9 | NS (S326C, P332A, 3); I (6) | ||
| UCSC | 11 | NS (S326C, P332A, P97A, P41A, S91C, 5); I (5); 3′UTR (1) | ||
| AceView | 19 | NS (S326C, S115C, S42C, P98A, P103A, P332A, 6); I (8); 3′UTR (4); 3down (1) | ||
| CAMK1 | RefSeq | 1 | 3down | |
| Ensembl | 2 | |||
| VEGA | 2 | |||
| UCSC | 3 | |||
| AceView | 8 | |||
| rs1130409 | APEX1 | RefSeq | 3 | NS (D148E, 3) |
| Ensembl | 2 | NS (D148E, 2) | ||
| VEGA | 3 | NS (D148E, 2); I (1) | ||
| UCSC | 4 | NS (D148E, 4) | ||
| AceView | 22 | NS (D148E, D124E, D130E, D131E, 13), I (4); 3′UTR (1); 5′UTR (1); 3down (3) | ||
| NP | RefSeq | – | ||
| Ensembl | 1 | I (1) | ||
| VEGA | – | |||
| UCSC | – | |||
| AceView | – | |||
| OSGEP | RefSeq | 1 | 5up | |
| Ensembl | 1 | |||
| VEGA | 1 | |||
| UCSC | 1 | |||
| AceView | 5 | |||
| TMEM55B | RefSeq | 2 | 3down | |
| Ensembl | 2 | |||
| VEGA | 2 | |||
| UCSC | 2 | |||
| AceView | 6 | |||
| rs2272615 | POLB | RefSeq | 1 | I (1) |
| Ensembl | 1 | I (1) | ||
| VEGA | 5 | I (5) | ||
| UCSC | 2 | I (2) | ||
| AceView | 8 | 3′UTR (1); 3down (1); I (6) | ||
| rs2953993 | POLB | RefSeq | 1 | I (1) |
| Ensembl | 1 | I (1) | ||
| VEGA | 6 | I (5); 5up (1) | ||
| UCSC | 2 | I (2) | ||
| AceView | 8 | I (8) | ||
| rs1799782 | XRCC1 | RefSeq | 1 | NS (R194W, 1) |
| Ensembl | 1 | NS (R194W, 1) | ||
| VEGA | 5 | NS (R194W, R157W, 5) | ||
| UCSC | 1 | NS (R194W, 1) | ||
| AceView | 9 | NS (R30W, R89W, R157W, R169W, R213W, R219W, R273W, 7); 5′UTR (2) | ||
| rs25487 | XRCC1 | RefSeq | 1 | NS (Q399R, 1) |
| Ensembl | 1 | NS (Q399R, 1) | ||
| VEGA | 5 | NS (Q399R, 1); 3down (4) | ||
| UCSC | 1 | NS (Q399R, 1) | ||
| AceView | 9 | NS (R126G, Q181R, Q235R, Q332R, Q422R, Q478R, 6); 3down (3) | ||
| rs2248690 | AHSG | RefSeq | 1 | 5up |
| Ensembl | 1 | |||
| VEGA | 2 | |||
| UCSC | 4 | |||
| AceView | 8 | |||
| rs4918 | AHSG | RefSeq | 1 | NS (S256T, 1) |
| Ensembl | 1 | NS (S256T, 1) | ||
| VEGA | 4 | NS (S256T, S255T, S9T, 3); 5′UTR (1) | ||
| UCSC | 3 | NS (S255T, S256T, S257T, 3) | ||
| AceView | 7 | NS (S219T, S228T, S255T, S256T, S257T, 5); 3down (2) | ||
| rs1071592 | AHSG | RefSeq | 1 | S (1) |
| Ensembl | 1 | S (1) | ||
| VEGA | 4 | NS (H6P, 1), S (2); 3down (1) | ||
| UCSC | 3 | S (3) | ||
| AceView | 6 | S (5); 3down (1) | ||
I=intronic, 5up=5-upstream, 3down=3-downstream, NS=coding non-synonymous, S=coding synonymous.