Impact of promoter SNPs on predicted transcription factor binding sites
| Gene, pSNP . | In silico predictions for TF binding sites . | Validated differential binding . | |||
|---|---|---|---|---|---|
| Gains (score*) . | Losses (score) . | HeLa . | Jeg-3 . | HepG2 . | |
| CDKN2A | |||||
| −222T>A | — | c-Myb (> 0.97), myogenin/nuclear factor 1 (> 0.74) | No | NA | No |
| CDKN2B | |||||
| −1270C>T | Interferon regulatory factor 2 (> 0.79), Pax1 paired domain protein (> 0.64) | B-cell–specific activating protein (> 0.79) | No | Yes | NA |
| −593A>T,C† | — | MyT1 zinc finger transcription factor (> 0.80), prostate-specific homeodomain protein NKX3.1 (0.84) | Yes | No | Yes |
| −287G>C | — | Neural-restrictive silencer element (0.70) | Yes | No | No |
| CDKN1A | |||||
| −1284T>C | — | — | No | Yes | Yes |
| −899T>G | v-Myb (> 0.92) | — | Yes | Yes | No |
| −791T>C | — | — | No | Yes | No |
| CDKN1B | |||||
| −1857C>T | Ecotropic viral integration site 1 encoded factor (> 0.83) | Myoblast determining factor (> 0.83) | No | Yes | No |
| −1608G>A | POZ/zinc finger protein (> 0.84) | — | No | No | No |
| −373G>T | GAGA-Box (> 0.78), olfactory neuron-specific factor (> 0.82), Pax1 paired domain protein (> 0.63), signal transducer and activator of transcription 1 (> 0.81), STAT6 (> 0.84) | Myc-associated zinc finger protein (> 0.94) | No | No | No |
| Gene, pSNP . | In silico predictions for TF binding sites . | Validated differential binding . | |||
|---|---|---|---|---|---|
| Gains (score*) . | Losses (score) . | HeLa . | Jeg-3 . | HepG2 . | |
| CDKN2A | |||||
| −222T>A | — | c-Myb (> 0.97), myogenin/nuclear factor 1 (> 0.74) | No | NA | No |
| CDKN2B | |||||
| −1270C>T | Interferon regulatory factor 2 (> 0.79), Pax1 paired domain protein (> 0.64) | B-cell–specific activating protein (> 0.79) | No | Yes | NA |
| −593A>T,C† | — | MyT1 zinc finger transcription factor (> 0.80), prostate-specific homeodomain protein NKX3.1 (0.84) | Yes | No | Yes |
| −287G>C | — | Neural-restrictive silencer element (0.70) | Yes | No | No |
| CDKN1A | |||||
| −1284T>C | — | — | No | Yes | Yes |
| −899T>G | v-Myb (> 0.92) | — | Yes | Yes | No |
| −791T>C | — | — | No | Yes | No |
| CDKN1B | |||||
| −1857C>T | Ecotropic viral integration site 1 encoded factor (> 0.83) | Myoblast determining factor (> 0.83) | No | Yes | No |
| −1608G>A | POZ/zinc finger protein (> 0.84) | — | No | No | No |
| −373G>T | GAGA-Box (> 0.78), olfactory neuron-specific factor (> 0.82), Pax1 paired domain protein (> 0.63), signal transducer and activator of transcription 1 (> 0.81), STAT6 (> 0.84) | Myc-associated zinc finger protein (> 0.94) | No | No | No |
Predicted impact of the pSNPs was estimated with the program matInspector. Gain and loss of transcription factor binding sites are specified for the minor allele with respect to the major allele. NA indicates not available; —, none.
Matrix similarity score.
Predictions for the minor allele −593T only are shown. In silico analysis for allele −593C was inconclusive.