Transcription factors with Perturb-seq knockdown data for LINC03040. 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 = LINC03040 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 LINC03040, 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 |
|---|---|---|---|---|
| chr6:43,998,451–43,998,914 | 1.7 kb | Proximal (<10kb) | 81 | |
| chr6:44,000,279–44,000,720 | at TSS | At TSS | 299 | |
| chr6:44,001,183–44,001,846 | 604 bp | At TSS | 357 | |
| chr6:44,002,061–44,003,708 | 1.5 kb | Proximal (<10kb) | 581 |
Genomic view of the LINC03040 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.