Transcription factors with Perturb-seq knockdown data for LINC01224. 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 = LINC01224 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 LINC01224, 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 |
|---|---|---|---|---|
| chr19:23,116,566–23,117,541 | 299.0 kb | Distal (>10kb) Multiome | 257 | |
| chr19:23,203,789–23,204,323 | 212.0 kb | Distal (>10kb) Multiome | 53 | |
| chr19:23,249,247–23,251,013 | 165.6 kb | Distal (>10kb) Multiome | 457 | |
| chr19:23,254,024–23,254,900 | 161.5 kb | Distal (>10kb) Multiome | 62 | |
| chr19:23,273,473–23,274,442 | 141.9 kb | Distal (>10kb) Multiome | 565 | |
| chr19:23,277,685–23,278,396 | 138.0 kb | Distal (>10kb) Multiome | 71 | |
| chr19:23,394,943–23,396,090 | 20.5 kb | Distal (>10kb) Multiome | 575 | |
| chr19:23,415,164–23,416,387 | 110 bp | At TSS Multiome | 222 | |
| chr19:23,420,932–23,421,175 | 4.9 kb | Proximal (<10kb) | 7 | |
| chr19:23,686,411–23,687,441 | 271.1 kb | Distal (>10kb) Multiome | 490 | |
| chr19:24,033,224–24,034,370 | 617.5 kb | Distal (>10kb) Multiome HiCAR | 673 |
Genomic view of the LINC01224 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.