Transcription factors with Perturb-seq knockdown data for SCN1A-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 = SCN1A-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 SCN1A-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 |
|---|---|---|---|---|
| chr2:165,697,835–165,698,908 | 258.6 kb | Distal (>10kb) Multiome | 259 | |
| chr2:165,793,126–165,795,058 | 162.9 kb | Distal (>10kb) Multiome | 703 | |
| chr2:165,952,696–165,953,070 | 4.1 kb | Proximal (<10kb) | 95 | |
| chr2:165,953,255–165,954,562 | 3.3 kb | Proximal (<10kb) Multiome | 1143 | |
| chr2:165,956,573–165,957,634 | at TSS | At TSS | 111 | |
| chr2:166,375,161–166,377,020 | 418.9 kb | Distal (>10kb) Multiome | 941 |
Genomic view of the SCN1A-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.