This gene is imprinted, with preferential expression of the maternal allele. The encoded protein is a tight-binding, strong inhibitor of several G1 cyclin/Cdk complexes and a negative regulator of cell proliferation. Mutations in this gene are implicated in sporadic cancers and Beckwith-Wiedemann syndorome, suggesting that this gene is a tumor suppressor candidate. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]
Transcription factors with Perturb-seq knockdown data for CDKN1C. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = CDKN1C upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CDKN1C, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr11:2,420,598–2,421,164 | 464.9 kb | Distal (>10kb) Multiome HiCAR | 385 | |
| chr11:2,444,173–2,445,584 | 440.9 kb | Distal (>10kb) Multiome HiCAR | 280 | |
| chr11:2,532,598–2,533,458 | 352.8 kb | Distal (>10kb) Multiome HiCAR | 567 | |
| chr11:2,693,272–2,694,189 | 192.2 kb | Distal (>10kb) Multiome HiCAR | 236 | |
| chr11:2,699,491–2,700,586 | 185.6 kb | Distal (>10kb) Multiome HiCAR | 879 | |
| chr11:2,862,328–2,863,500 | 23.2 kb | Distal (>10kb) Multiome | 132 | |
| chr11:2,882,619–2,883,133 | 2.6 kb | Proximal (<10kb) | 54 | |
| chr11:2,883,795–2,886,948 | 178 bp | At TSS Multiome | 639 | |
| chr11:2,888,443–2,888,665 | 2.7 kb | Proximal (<10kb) | 345 | |
| chr11:2,891,828–2,893,111 | 6.7 kb | Proximal (<10kb) Multiome | 572 | |
| chr11:2,901,621–2,903,073 | 16.4 kb | Distal (>10kb) Multiome | 610 | |
| chr11:2,928,807–2,931,249 | 45.1 kb | Distal (>10kb) Multiome | 770 | |
| chr11:2,991,519–2,993,201 | 106.6 kb | Distal (>10kb) Multiome | 759 | |
| chr11:3,056,953–3,057,972 | 171.8 kb | Distal (>10kb) Multiome | 798 | |
| chr11:3,091,645–3,092,317 | 206.2 kb | Distal (>10kb) Multiome | 449 | |
| chr11:3,148,512–3,149,454 | 263.2 kb | Distal (>10kb) Multiome | 152 | |
| chr11:3,160,043–3,161,026 | 274.7 kb | Distal (>10kb) Multiome | 283 | |
| chr11:3,164,925–3,165,485 | 279.5 kb | Distal (>10kb) Multiome | 326 |
Genomic view of the CDKN1C locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.