Transcription factors with Perturb-seq knockdown data for SYT9-AS1. 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 = SYT9-AS1 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 SYT9-AS1, 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 |
|---|---|---|---|---|
| chr11:7,251,328–7,253,026 | 261.7 kb | Distal (>10kb) Multiome | 423 | |
| chr11:7,507,737–7,508,506 | 5.7 kb | Proximal (<10kb) Multiome | 150 | |
| chr11:7,512,733–7,514,729 | 129 bp | At TSS Multiome | 725 | |
| chr11:7,571,498–7,572,368 | 58.2 kb | Distal (>10kb) Multiome | 461 | |
| chr11:7,573,550–7,574,414 | 60.3 kb | Distal (>10kb) Multiome | 486 | |
| chr11:7,672,897–7,674,787 | 159.9 kb | Distal (>10kb) Multiome | 379 |
Genomic view of the SYT9-AS1 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.