Transcription factors with Perturb-seq knockdown data for LINC00649. 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 = LINC00649 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 LINC00649, 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 |
|---|---|---|---|---|
| chr21:33,641,108–33,643,411 | 273.8 kb | Distal (>10kb) Multiome | 1018 | |
| chr21:33,894,789–33,895,286 | 20.9 kb | Distal (>10kb) Multiome | 371 | |
| chr21:33,915,370–33,916,223 | 26 bp | At TSS Multiome | 730 | |
| chr21:33,924,057–33,924,312 | 8.2 kb | Proximal (<10kb) | 396 | |
| chr21:34,072,589–34,075,396 | 159.1 kb | Distal (>10kb) Multiome HiCAR | 822 | |
| chr21:34,201,488–34,202,922 | 286.2 kb | Distal (>10kb) Multiome | 669 |
Genomic view of the LINC00649 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.