Transcription factors with Perturb-seq knockdown data for LINC01993. 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 = LINC01993 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 LINC01993, 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 |
|---|---|---|---|---|
| chr17:78,127,361–78,129,338 | 149.7 kb | Distal (>10kb) Multiome | 909 | |
| chr17:78,140,136–78,141,130 | 137.9 kb | Distal (>10kb) Multiome | 594 | |
| chr17:78,168,117–78,169,078 | 110.0 kb | Distal (>10kb) Multiome | 738 | |
| chr17:78,186,463–78,187,739 | 91.3 kb | Distal (>10kb) Multiome | 1021 | |
| chr17:78,213,978–78,214,702 | 64.3 kb | Distal (>10kb) Multiome | 902 | |
| chr17:78,250,689–78,251,651 | 27.4 kb | Distal (>10kb) Multiome | 714 | |
| chr17:78,254,178–78,254,892 | 24.0 kb | Distal (>10kb) Multiome | 860 | |
| chr17:78,268,939–78,269,694 | 8.8 kb | Proximal (<10kb) | 214 | |
| chr17:78,270,255–78,273,257 | 6.1 kb | Proximal (<10kb) Multiome | 667 | |
| chr17:78,278,089–78,278,902 | 34 bp | At TSS Multiome | 225 | |
| chr17:78,313,762–78,314,579 | 35.8 kb | Distal (>10kb) Multiome | 636 | |
| chr17:78,341,604–78,342,374 | 63.5 kb | Distal (>10kb) Multiome HiCAR | 423 | |
| chr17:78,352,598–78,353,774 | 74.6 kb | Distal (>10kb) Multiome HiCAR | 687 | |
| chr17:78,358,869–78,361,525 | 81.8 kb | Distal (>10kb) Multiome HiCAR | 898 | |
| chr17:78,365,478–78,366,101 | 87.4 kb | Distal (>10kb) Multiome HiCAR | 305 | |
| chr17:78,378,324–78,379,091 | 100.1 kb | Distal (>10kb) Multiome | 921 |
Genomic view of the LINC01993 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.