Transcription factors with Perturb-seq knockdown data for LINC00678. 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 = LINC00678 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 LINC00678, 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 |
|---|---|---|---|---|
| chr11:27,362,704–27,363,814 | 271.4 kb | Distal (>10kb) Multiome | 933 | |
| chr11:27,443,724–27,444,393 | 190.7 kb | Distal (>10kb) Multiome | 91 | |
| chr11:27,444,522–27,445,324 | 189.5 kb | Distal (>10kb) Multiome | 199 | |
| chr11:27,471,035–27,473,509 | 161.8 kb | Distal (>10kb) Multiome | 780 | |
| chr11:27,506,080–27,507,386 | 127.8 kb | Distal (>10kb) Multiome | 861 | |
| chr11:27,625,016–27,625,854 | 8.8 kb | Proximal (<10kb) | 45 | |
| chr11:27,625,986–27,626,116 | 8.5 kb | Proximal (<10kb) | 10 | |
| chr11:27,626,348–27,627,487 | 7.1 kb | Proximal (<10kb) | 70 | |
| chr11:27,628,672–27,629,755 | 5.3 kb | Proximal (<10kb) Multiome | 92 | |
| chr11:27,632,311–27,632,671 | 2.0 kb | Proximal (<10kb) | 2 | |
| chr11:27,632,781–27,633,249 | 1.4 kb | Proximal (<10kb) | 69 | |
| chr11:27,634,338–27,635,109 | 187 bp | At TSS Multiome | 115 | |
| chr11:27,635,718–27,636,112 | 1.1 kb | Proximal (<10kb) | 59 | |
| chr11:27,698,739–27,701,728 | 66.2 kb | Distal (>10kb) Multiome | 518 | |
| chr11:27,718,043–27,719,845 | 84.2 kb | Distal (>10kb) Multiome | 477 | |
| chr11:27,721,736–27,723,344 | 88.1 kb | Distal (>10kb) Multiome | 381 | |
| chr11:27,795,831–27,797,062 | 161.9 kb | Distal (>10kb) Multiome | 361 |
Genomic view of the LINC00678 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.