Transcription factors with Perturb-seq knockdown data for LINC01963. 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 = LINC01963 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 LINC01963, 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 |
|---|---|---|---|---|
| chr2:216,012,871–216,013,914 | 203.6 kb | Distal (>10kb) Multiome | 664 | |
| chr2:216,081,343–216,082,368 | 135.2 kb | Distal (>10kb) Multiome | 872 | |
| chr2:216,109,035–216,110,011 | 107.7 kb | Distal (>10kb) Multiome | 866 | |
| chr2:216,114,288–216,115,514 | 102.1 kb | Distal (>10kb) Multiome | 671 | |
| chr2:216,216,039–216,216,260 | 784 bp | At TSS | 57 | |
| chr2:216,283,571–216,284,041 | 66.7 kb | Distal (>10kb) Multiome | 206 | |
| chr2:216,339,679–216,340,452 | 123.1 kb | Distal (>10kb) Multiome | 192 | |
| chr2:216,370,964–216,372,465 | 154.2 kb | Distal (>10kb) Multiome | 850 | |
| chr2:216,412,020–216,413,196 | 195.5 kb | Distal (>10kb) Multiome | 882 | |
| chr2:216,498,326–216,499,289 | 281.8 kb | Distal (>10kb) Multiome | 982 |
Genomic view of the LINC01963 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.