Transcription factors with Perturb-seq knockdown data for TSPEAR-AS2. 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 = TSPEAR-AS2 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 TSPEAR-AS2, 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 |
|---|---|---|---|---|
| chr21:44,283,183–44,283,881 | 233.8 kb | Distal (>10kb) Multiome | 19 | |
| chr21:44,299,485–44,300,902 | 217.2 kb | Distal (>10kb) Multiome | 730 | |
| chr21:44,338,994–44,339,895 | 178.0 kb | Distal (>10kb) Multiome | 904 | |
| chr21:44,341,372–44,342,456 | 175.2 kb | Distal (>10kb) Multiome | 87 | |
| chr21:44,454,821–44,456,545 | 61.9 kb | Distal (>10kb) Multiome | 481 | |
| chr21:44,510,378–44,510,951 | 6.5 kb | Proximal (<10kb) Multiome | 473 | |
| chr21:44,686,253–44,687,168 | 169.4 kb | Distal (>10kb) Multiome HiCAR | 199 | |
| chr21:44,711,499–44,711,908 | 194.5 kb | Distal (>10kb) Multiome HiCAR | 168 | |
| chr21:44,748,550–44,748,985 | 231.7 kb | Distal (>10kb) Multiome HiCAR | 149 | |
| chr21:44,801,527–44,802,290 | 284.7 kb | Distal (>10kb) Multiome HiCAR | 818 |
Genomic view of the TSPEAR-AS2 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.