Transcription factors with Perturb-seq knockdown data for HIF1A-AS3. 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 = HIF1A-AS3 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 HIF1A-AS3, 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 |
|---|---|---|---|---|
| chr14:61,427,068–61,427,986 | 323.7 kb | Distal (>10kb) Multiome | 9 | |
| chr14:61,567,895–61,569,162 | 182.3 kb | Distal (>10kb) Multiome | 399 | |
| chr14:61,601,551–61,603,283 | 149.0 kb | Distal (>10kb) Multiome | 299 | |
| chr14:61,694,796–61,696,447 | 55.7 kb | Distal (>10kb) Multiome | 933 | |
| chr14:61,749,921–61,750,153 | 902 bp | At TSS | 177 | |
| chr14:61,750,867–61,751,496 | 128 bp | At TSS Multiome | 529 | |
| chr14:61,753,632–61,753,809 | 2.6 kb | Proximal (<10kb) | 64 | |
| chr14:61,761,767–61,763,093 | 11.3 kb | Distal (>10kb) Multiome | 643 | |
| chr14:61,812,101–61,813,600 | 61.7 kb | Distal (>10kb) Multiome | 261 |
Genomic view of the HIF1A-AS3 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.