Transcription factors with Perturb-seq knockdown data for TPT1-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 = TPT1-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 TPT1-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 |
|---|---|---|---|---|
| chr13:45,048,778–45,049,467 | 292.2 kb | Distal (>10kb) Multiome HiCAR | 140 | |
| chr13:45,120,138–45,120,985 | 220.9 kb | Distal (>10kb) Multiome | 723 | |
| chr13:45,249,481–45,250,367 | 91.5 kb | Distal (>10kb) Multiome | 120 | |
| chr13:45,310,992–45,312,067 | 30.0 kb | Distal (>10kb) Multiome | 340 | |
| chr13:45,331,176–45,331,542 | 9.9 kb | Proximal (<10kb) | 117 | |
| chr13:45,332,996–45,333,477 | 7.9 kb | Proximal (<10kb) | 85 | |
| chr13:45,340,420–45,342,118 | 9 bp | At TSS Multiome | 982 | |
| chr13:45,369,205–45,369,799 | 28.1 kb | Distal (>10kb) Multiome | 26 | |
| chr13:45,370,842–45,371,300 | 29.7 kb | Distal (>10kb) Multiome | 284 | |
| chr13:45,396,133–45,396,998 | 55.3 kb | Distal (>10kb) Multiome | 148 | |
| chr13:45,417,648–45,418,935 | 77.1 kb | Distal (>10kb) Multiome | 793 | |
| chr13:45,464,608–45,465,647 | 123.6 kb | Distal (>10kb) Multiome | 854 |
Genomic view of the TPT1-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.