Transcription factors with Perturb-seq knockdown data for LINC01612. 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 = LINC01612 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 LINC01612, 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 |
|---|---|---|---|---|
| chr4:169,934,787–169,935,471 | 291.6 kb | Distal (>10kb) Multiome | 121 | |
| chr4:170,004,428–170,005,171 | 221.8 kb | Distal (>10kb) Multiome | 112 | |
| chr4:170,025,638–170,027,809 | 200.1 kb | Distal (>10kb) Multiome | 968 | |
| chr4:170,089,100–170,090,754 | 136.4 kb | Distal (>10kb) Multiome | 761 | |
| chr4:170,109,620–170,111,763 | 116.0 kb | Distal (>10kb) Multiome | 267 | |
| chr4:170,226,061–170,226,737 | at TSS | At TSS | 104 | |
| chr4:170,227,932–170,228,228 | 1.3 kb | Proximal (<10kb) | 10 | |
| chr4:170,229,082–170,229,302 | 2.5 kb | Proximal (<10kb) | 31 | |
| chr4:170,230,365–170,231,741 | 3.8 kb | Proximal (<10kb) | 91 | |
| chr4:170,259,234–170,260,354 | 33.2 kb | Distal (>10kb) Multiome | 326 | |
| chr4:170,285,465–170,286,907 | 59.5 kb | Distal (>10kb) Multiome | 211 |
Genomic view of the LINC01612 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.