Transcription factors with Perturb-seq knockdown data for BCAR3-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 = BCAR3-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 BCAR3-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 |
|---|---|---|---|---|
| chr1:93,345,396–93,346,457 | 246.1 kb | Distal (>10kb) Multiome | 1003 | |
| chr1:93,447,560–93,449,029 | 143.9 kb | Distal (>10kb) Multiome | 726 | |
| chr1:93,474,058–93,474,810 | 117.6 kb | Distal (>10kb) Multiome | 63 | |
| chr1:93,484,155–93,485,250 | 107.2 kb | Distal (>10kb) Multiome | 146 | |
| chr1:93,591,732–93,592,238 | at TSS | At TSS | 612 | |
| chr1:93,622,085–93,622,775 | 30.4 kb | Distal (>10kb) Multiome | 282 | |
| chr1:93,678,776–93,679,511 | 87.3 kb | Distal (>10kb) Multiome | 96 | |
| chr1:93,680,733–93,682,277 | 90.0 kb | Distal (>10kb) Multiome | 717 | |
| chr1:93,814,055–93,816,005 | 223.3 kb | Distal (>10kb) Multiome HiCAR | 533 | |
| chr1:93,820,560–93,821,453 | 229.1 kb | Distal (>10kb) Multiome HiCAR | 160 | |
| chr1:93,845,985–93,846,892 | 254.3 kb | Distal (>10kb) Multiome HiCAR | 732 | |
| chr1:93,846,995–93,848,315 | 255.6 kb | Distal (>10kb) Multiome HiCAR | 954 | |
| chr1:93,878,726–93,879,400 | 287.2 kb | Distal (>10kb) Multiome | 851 |
Genomic view of the BCAR3-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.