Transcription factors with Perturb-seq knockdown data for LINC02474. 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 = LINC02474 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 LINC02474, 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 |
|---|---|---|---|---|
| chr1:220,809,823–220,810,852 | 1155.9 kb | Distal (>10kb) Multiome HiCAR | 265 | |
| chr1:221,510,825–221,512,374 | 454.4 kb | Distal (>10kb) Multiome HiCAR | 216 | |
| chr1:221,741,206–221,744,237 | 224.1 kb | Distal (>10kb) Multiome HiCAR | 1085 | |
| chr1:221,964,631–221,965,405 | 1.4 kb | Proximal (<10kb) Multiome | 94 | |
| chr1:221,965,763–221,966,471 | 162 bp | At TSS Multiome | 27 | |
| chr1:221,967,531–221,967,855 | 1.2 kb | Proximal (<10kb) | 47 | |
| chr1:221,971,199–221,971,743 | 4.9 kb | Proximal (<10kb) | 14 | |
| chr1:221,972,131–221,972,883 | 5.8 kb | Proximal (<10kb) | 66 | |
| chr1:221,973,101–221,973,459 | 6.8 kb | Proximal (<10kb) | 14 | |
| chr1:222,028,164–222,028,641 | 62.0 kb | Distal (>10kb) Multiome | 97 | |
| chr1:222,031,101–222,031,767 | 65.1 kb | Distal (>10kb) Multiome | 98 |
Genomic view of the LINC02474 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.