Transcription factors with Perturb-seq knockdown data for RTL6. 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 = RTL6 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 RTL6, 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 |
|---|---|---|---|---|
| chr22:44,331,085–44,331,548 | 166.8 kb | Distal (>10kb) Multiome | 128 | |
| chr22:44,497,886–44,498,569 | 89 bp | At TSS Multiome | 437 | |
| chr22:44,661,031–44,661,516 | 163.0 kb | Distal (>10kb) Multiome | 28 | |
| chr22:44,668,163–44,669,181 | 170.3 kb | Distal (>10kb) Multiome | 265 | |
| chr22:44,684,755–44,685,227 | 186.7 kb | Distal (>10kb) Multiome | 562 | |
| chr22:44,701,628–44,703,097 | 203.9 kb | Distal (>10kb) Multiome | 588 | |
| chr22:44,752,293–44,752,996 | 254.3 kb | Distal (>10kb) Multiome | 233 |
Genomic view of the RTL6 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.