Transcription factors with Perturb-seq knockdown data for VLDLR-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 = VLDLR-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 VLDLR-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 |
|---|---|---|---|---|
| chr9:2,241,108–2,243,366 | 379.5 kb | Distal (>10kb) Multiome HiCAR | 876 | |
| chr9:2,280,841–2,282,179 | 340.0 kb | Distal (>10kb) Multiome HiCAR | 259 | |
| chr9:2,283,300–2,283,939 | 337.8 kb | Distal (>10kb) Multiome HiCAR | 77 | |
| chr9:2,420,269–2,421,188 | 200.7 kb | Distal (>10kb) Multiome HiCAR | 122 | |
| chr9:2,537,107–2,538,712 | 83.3 kb | Distal (>10kb) Multiome | 82 | |
| chr9:2,613,640–2,614,231 | 7.2 kb | Proximal (<10kb) | 78 | |
| chr9:2,620,982–2,623,801 | 173 bp | At TSS Multiome | 768 | |
| chr9:2,745,497–2,746,547 | 124.4 kb | Distal (>10kb) Multiome | 205 | |
| chr9:2,764,803–2,765,871 | 143.8 kb | Distal (>10kb) Multiome | 210 | |
| chr9:2,770,773–2,771,918 | 149.8 kb | Distal (>10kb) Multiome | 272 | |
| chr9:2,816,339–2,817,126 | 195.3 kb | Distal (>10kb) Multiome | 152 | |
| chr9:2,843,166–2,844,741 | 222.8 kb | Distal (>10kb) Multiome | 860 |
Genomic view of the VLDLR-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.