Transcription factors with Perturb-seq knockdown data for LINC02406. 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 = LINC02406 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 LINC02406, 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 |
|---|---|---|---|---|
| chr12:38,904,541–38,907,396 | 238.7 kb | Distal (>10kb) Multiome | 887 | |
| chr12:39,029,063–39,030,001 | 116.1 kb | Distal (>10kb) Multiome | 84 | |
| chr12:39,122,188–39,123,439 | 22.7 kb | Distal (>10kb) Multiome | 162 | |
| chr12:39,138,349–39,138,707 | 6.8 kb | Proximal (<10kb) | 85 | |
| chr12:39,144,543–39,145,917 | 1 bp | At TSS Multiome | 349 | |
| chr12:39,442,123–39,444,400 | 297.8 kb | Distal (>10kb) Multiome | 954 |
Genomic view of the LINC02406 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.