Transcription factors with Perturb-seq knockdown data for LINC02609. 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 = LINC02609 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 LINC02609, 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 |
|---|---|---|---|---|
| chr1:90,706,413–90,707,856 | 128.8 kb | Distal (>10kb) Multiome | 417 | |
| chr1:90,717,468–90,719,506 | 118.1 kb | Distal (>10kb) Multiome | 387 | |
| chr1:90,723,557–90,724,199 | 112.3 kb | Distal (>10kb) Multiome HiCAR | 186 | |
| chr1:90,729,370–90,729,963 | 106.5 kb | Distal (>10kb) Multiome HiCAR | 164 | |
| chr1:90,826,876–90,827,347 | 8.2 kb | Proximal (<10kb) | 100 | |
| chr1:90,833,266–90,836,598 | 1.1 kb | Proximal (<10kb) Multiome | 374 | |
| chr1:90,841,491–90,842,027 | 5.9 kb | Proximal (<10kb) | 70 | |
| chr1:90,850,622–90,852,216 | 15.5 kb | Distal (>10kb) Multiome | 712 | |
| chr1:91,021,015–91,022,673 | 185.7 kb | Distal (>10kb) Multiome | 1058 |
Genomic view of the LINC02609 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.