Transcription factors with Perturb-seq knockdown data for RYBP. 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 = RYBP 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 RYBP, 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 |
|---|---|---|---|---|
| chr3:72,334,933–72,335,840 | 111.2 kb | Distal (>10kb) Multiome | 175 | |
| chr3:72,446,472–72,448,000 | 618 bp | At TSS Multiome | 763 | |
| chr3:72,451,627–72,452,103 | 5.0 kb | Proximal (<10kb) | 27 | |
| chr3:72,452,711–72,452,966 | 6.1 kb | Proximal (<10kb) | 67 | |
| chr3:72,665,704–72,666,421 | 219.4 kb | Distal (>10kb) Multiome | 244 | |
| chr3:72,738,568–72,739,351 | 292.3 kb | Distal (>10kb) Multiome | 226 | |
| chr3:72,743,925–72,744,951 | 297.8 kb | Distal (>10kb) Multiome | 287 |
Genomic view of the RYBP 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.