Transcription factors with Perturb-seq knockdown data for VIM-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 = VIM-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 VIM-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 |
|---|---|---|---|---|
| chr10:15,859,871–15,860,810 | 1369.6 kb | Distal (>10kb) Multiome HiCAR | 695 | |
| chr10:16,891,324–16,892,326 | 338.4 kb | Distal (>10kb) Multiome HiCAR | 599 | |
| chr10:16,962,424–16,962,891 | 267.4 kb | Distal (>10kb) Multiome | 31 | |
| chr10:17,200,899–17,202,136 | 28.5 kb | Distal (>10kb) Multiome | 1040 | |
| chr10:17,228,175–17,230,908 | 1.0 kb | Proximal (<10kb) Multiome | 920 | |
| chr10:17,379,036–17,380,059 | 149.4 kb | Distal (>10kb) Multiome | 120 | |
| chr10:17,387,758–17,388,950 | 158.3 kb | Distal (>10kb) Multiome | 319 | |
| chr10:17,453,122–17,455,034 | 224.4 kb | Distal (>10kb) Multiome | 584 |
Genomic view of the VIM-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.