Transcription factors with Perturb-seq knockdown data for SHROOM3-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 = SHROOM3-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 SHROOM3-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 |
|---|---|---|---|---|
| chr4:76,585,845–76,586,672 | 216.3 kb | Distal (>10kb) Multiome | 423 | |
| chr4:76,590,067–76,590,517 | 212.1 kb | Distal (>10kb) Multiome | 287 | |
| chr4:76,689,137–76,689,934 | 113.0 kb | Distal (>10kb) Multiome | 423 | |
| chr4:76,748,807–76,748,959 | 9.5 kb | Proximal (<10kb) | 114 | |
| chr4:76,758,382–76,758,581 | at TSS | At TSS | 95 | |
| chr4:76,801,591–76,802,890 | at TSS | At TSS | 200 | |
| chr4:76,867,647–76,869,012 | 65.9 kb | Distal (>10kb) Multiome | 115 | |
| chr4:76,896,697–76,898,709 | 95.8 kb | Distal (>10kb) Multiome | 498 | |
| chr4:76,948,267–76,951,238 | 147.2 kb | Distal (>10kb) Multiome | 968 | |
| chr4:77,074,968–77,076,780 | 273.0 kb | Distal (>10kb) Multiome | 1071 |
Genomic view of the SHROOM3-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.