Table 1 List of oligonucleotide probes tested in EMSA
From: Regulatory single nucleotide polymorphisms (rSNPs) at the promoters 1A and 1B of the human APC gene
SNP identifier in dbSNP NCBI database | Sequences of oligonucleotides 5’- > 3’ | Coordinates (hg19) | Minor Allele Count (MAF) | Promoter |
|---|---|---|---|---|
Rs75612255: T > C | Allele T: ATTTATTACTCTCCCTCCCACCTCCGGCATC Allele C: ATTTATTACTCTCCCCCCCACCTCCGGCATC | Chr5:112737543 (−316), 5'-flank | NA | 1A |
Rs79734816: T > C | Allele T: TCTGCCCTGCGGACCTCCCCCGACTCTTTAC Allele C: TCTGCCCTGCGGACCCCCCCCGACTCTTTAC | Chr5: 112737587 (−272), 5'-flank | NA | 1A |
Rs77733015: T > G | Allele T: GGGCTAGGCAGGCTGTGCGGTTGGGCGGGGC Allele G: GGGCTAGGCAGGCTGGGCGGTTGGGCGGGGC | Chr5: 112737699 (−160), 5'-flank | NA | 1A |
Rs78597499: T > G | Allele T: AGGCAGGCTGTGCGGTTGGGCGGGGCCCTGT Allele G: AGGCAGGCTGTGCGGGTGGGCGGGGCCCTGT | Chr5: 112737704 (−155), 5'-flank | NA | 1A |
Rs35417795: 112737713delG | Allele del: GTGCGGTTGGGCGGG-CCCTGTGCCCCACTG Allele G: GTGCGGTTGGGCGGGGCCCTGTGCCCCACTG | Chr5: 112737713 (−146), 5'-flank | NA | 1A |
Rs113017087: T > C | Allele T: GTGTAATCCGCTGGATGCGGACCAGGGCGCT Allele C: GTGTAATCCGCTGGACGCGGACCAGGGCGCT | Chr5: 112737780 (−79), 5'-flank | C = 0.0032/16 | 1A |
Rs75996864: T > G | Allele C: ACCGACATGTGGCTGTATTGGTGCAGCCCGC Allele G: ACCGACATGTGGCTGGATTGGTGCAGCCCGC | Chr5: 112737860 (1), 5'-UTR | NA | 1A |
Rs115242894: G > C | Allele G: GTATTGGTGCAGCCCGCCAGGGTGTCACTGG Allele C: GTATTGGTGCAGCCCCCCAGGGTGTCACTGG | Chr5: 112737874 (15), 5'-UTR | C = 0.0042/21 | 1A |
Rs80112297: A > G | Allele A: GCTTGCTGCGGGGGGAGGGGGGAAGGTGGTT Allele G: GCTTGCTGCGGGGGGGGGGGGGAAGGTGGTT | Chr5: 112737967 (108), intron | NA | 1A |
Rs76241113: A > G | Allele A: GCGGGGGGAGGGGGGAAGGTGGTTTTCCCTC Allele G: GCGGGGGGAGGGGGGGAGGTGGTTTTCCCTC | Chr5: 112737974 (115), intron | NA | 1A |
Rs80313086: T > G | Allele T: GGGGAGGGGGGAAGGTGGTTTTCCCTCGCAC Allele G: GGGGAGGGGGGAAGGGGGTTTTCCCTCGCAC | Chr5: 112737978 (119), intron | NA | 1A |
Rs115658307: C > T | Allele C: CAAGATGGCGGAGGGCAAGTAGCAAGGGGGC Allele T: CAAGATGGCGGAGGGTAAGTAGCAAGGGGGC | Chr5: 112707537 (33), 5'-UTR | T = 0.0054/27 | 1B |
Rs138386816: C > T | Allele C: GCGGGGTGTGGCCGCCGGAAGCCTAGCCGCT Allele T: GCGGGGTGTGGCCGCTGGAAGCCTAGCCGCT | Chr5: 112707566 (62), 5'-UTR | T = 0.0088/44 | 1B |
Rs79896135: C > G | Allele C: AGCCTAGCCGCTGCTCGGGGGGGACCTGCGG Allele G: AGCCTAGCCGCTGCTGGGGGGGGACCTGCGG | Chr5: 112707585 (81), 5'-UTR | G = 0.1777/890 | 1B |
Rs78429131: T > G | Allele T: AGGAAGGTGAAGCACTCAGTTGCCTTCTCGG Allele G: AGGAAGGTGAAGCACGCAGTTGCCTTCTCGG | Chr5: 112707687 (183), 5'-UTR | G = 0.0767/384 | 1B |