Transcription factors with Perturb-seq knockdown data for LINC01475. 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 = LINC01475 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 LINC01475, 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 |
|---|---|---|---|---|
| chr10:99,519,844–99,520,769 | 6.7 kb | Proximal (<10kb) | 331 | |
| chr10:99,521,296–99,522,437 | 5.0 kb | Proximal (<10kb) | 252 | |
| chr10:99,522,567–99,524,013 | 3.4 kb | Proximal (<10kb) | 201 | |
| chr10:99,524,178–99,524,594 | 2.8 kb | Proximal (<10kb) | 87 | |
| chr10:99,524,765–99,525,305 | 2.1 kb | Proximal (<10kb) | 50 | |
| chr10:99,527,131–99,527,911 | at TSS | At TSS | 89 | |
| chr10:99,530,180–99,530,606 | 2.7 kb | Proximal (<10kb) | 75 | |
| chr10:99,531,091–99,531,503 | 3.6 kb | Proximal (<10kb) | 112 | |
| chr10:99,532,575–99,533,287 | 5.1 kb | Proximal (<10kb) | 160 | |
| chr10:99,534,863–99,536,063 | 7.4 kb | Proximal (<10kb) | 193 | |
| chr10:99,536,574–99,538,002 | 9.1 kb | Proximal (<10kb) | 279 | |
| chr10:99,540,571–99,541,130 | 9.4 kb | Proximal (<10kb) | 218 |
Genomic view of the LINC01475 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.