Transcription factors with Perturb-seq knockdown data for HRG-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 = HRG-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 HRG-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 |
|---|---|---|---|---|
| chr3:186,566,830–186,567,930 | 205.6 kb | Distal (>10kb) Multiome | 850 | |
| chr3:186,570,047–186,571,165 | 202.5 kb | Distal (>10kb) Multiome HiCAR | 735 | |
| chr3:186,653,868–186,654,549 | 118.8 kb | Distal (>10kb) Multiome | 163 | |
| chr3:186,753,266–186,753,427 | 4.3 kb | Proximal (<10kb) | 304 | |
| chr3:186,757,705–186,757,993 | at TSS | At TSS | 45 | |
| chr3:186,772,788–186,773,308 | 24 bp | At TSS Multiome | 241 | |
| chr3:186,775,941–186,776,679 | 3.2 kb | Proximal (<10kb) Multiome | 161 | |
| chr3:186,782,866–186,784,510 | 10.4 kb | Distal (>10kb) Multiome | 1121 | |
| chr3:186,806,142–186,807,252 | 33.6 kb | Distal (>10kb) Multiome | 877 | |
| chr3:186,824,344–186,826,061 | 52.6 kb | Distal (>10kb) Multiome | 328 | |
| chr3:186,827,252–186,828,058 | 54.6 kb | Distal (>10kb) Multiome | 539 | |
| chr3:186,929,799–186,932,446 | 158.4 kb | Distal (>10kb) Multiome | 861 | |
| chr3:186,998,752–186,999,772 | 226.2 kb | Distal (>10kb) Multiome | 215 |
Genomic view of the HRG-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.