Transcription factors with Perturb-seq knockdown data for LINC03049. 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 = LINC03049 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 LINC03049, 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 |
|---|---|---|---|---|
| chr19:34,676,923–34,678,053 | 173.2 kb | Distal (>10kb) Multiome | 728 | |
| chr19:34,733,416–34,734,655 | 116.6 kb | Distal (>10kb) Multiome | 1008 | |
| chr19:34,772,709–34,773,413 | 77.6 kb | Distal (>10kb) Multiome | 680 | |
| chr19:34,920,040–34,921,057 | 69.7 kb | Distal (>10kb) Multiome | 309 | |
| chr19:34,926,731–34,927,343 | 76.2 kb | Distal (>10kb) Multiome | 741 | |
| chr19:34,963,909–34,964,414 | 113.4 kb | Distal (>10kb) Multiome HiCAR | 645 | |
| chr19:34,999,304–35,000,970 | 149.4 kb | Distal (>10kb) Multiome | 759 | |
| chr19:35,030,124–35,031,270 | 179.8 kb | Distal (>10kb) Multiome | 534 | |
| chr19:35,040,969–35,041,953 | 190.8 kb | Distal (>10kb) Multiome | 806 | |
| chr19:35,055,754–35,056,570 | 205.2 kb | Distal (>10kb) Multiome | 268 | |
| chr19:35,090,562–35,091,150 | 240.0 kb | Distal (>10kb) Multiome | 303 | |
| chr19:35,135,242–35,135,695 | 284.8 kb | Distal (>10kb) Multiome | 525 | |
| chr19:35,140,763–35,141,948 | 290.6 kb | Distal (>10kb) Multiome | 509 | |
| chr19:35,142,085–35,143,541 | 292.2 kb | Distal (>10kb) Multiome | 328 |
Genomic view of the LINC03049 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.