Transcription factors with Perturb-seq knockdown data for LINC02608. 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 = LINC02608 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 LINC02608, 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 |
|---|---|---|---|---|
| chr1:212,034,569–212,036,407 | 249.7 kb | Distal (>10kb) Multiome | 995 | |
| chr1:212,214,185–212,214,767 | 70.5 kb | Distal (>10kb) Multiome | 99 | |
| chr1:212,238,550–212,239,130 | at TSS | At TSS | 151 | |
| chr1:212,284,406–212,286,816 | 13 bp | At TSS Multiome | 1049 | |
| chr1:212,291,557–212,291,757 | 6.4 kb | Proximal (<10kb) | 228 | |
| chr1:212,309,881–212,310,794 | 25.1 kb | Distal (>10kb) Multiome | 183 | |
| chr1:212,315,914–212,316,445 | 31.0 kb | Distal (>10kb) Multiome | 140 | |
| chr1:212,413,972–212,416,004 | 129.8 kb | Distal (>10kb) Multiome | 833 | |
| chr1:212,432,597–212,433,702 | 147.8 kb | Distal (>10kb) Multiome | 576 | |
| chr1:212,477,008–212,477,651 | 192.2 kb | Distal (>10kb) Multiome | 419 | |
| chr1:212,498,151–212,499,452 | 213.8 kb | Distal (>10kb) Multiome | 216 | |
| chr1:212,514,035–212,515,926 | 230.3 kb | Distal (>10kb) Multiome | 524 | |
| chr1:212,558,067–212,559,384 | 273.9 kb | Distal (>10kb) Multiome | 891 |
Genomic view of the LINC02608 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.