Transcription factors with Perturb-seq knockdown data for CCNY-AS1. 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 = CCNY-AS1 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 CCNY-AS1, 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 |
|---|---|---|---|---|
| chr10:35,089,654–35,090,939 | 246.0 kb | Distal (>10kb) Multiome | 797 | |
| chr10:35,126,359–35,127,943 | 209.5 kb | Distal (>10kb) Multiome | 1045 | |
| chr10:35,329,614–35,330,041 | 6.4 kb | Proximal (<10kb) | 35 | |
| chr10:35,335,922–35,337,633 | 78 bp | At TSS Multiome | 701 | |
| chr10:35,384,192–35,385,102 | 48.1 kb | Distal (>10kb) Multiome | 160 | |
| chr10:35,414,119–35,414,985 | 78.1 kb | Distal (>10kb) Multiome | 293 | |
| chr10:35,594,207–35,595,110 | 258.3 kb | Distal (>10kb) Multiome | 159 | |
| chr10:35,632,784–35,636,269 | 297.0 kb | Distal (>10kb) Multiome | 363 |
Genomic view of the CCNY-AS1 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.