Transcription factors with Perturb-seq knockdown data for DDN-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 = DDN-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 DDN-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 |
|---|---|---|---|---|
| chr12:48,788,600–48,789,901 | 229.6 kb | Distal (>10kb) Multiome | 478 | |
| chr12:48,795,703–48,796,330 | 222.9 kb | Distal (>10kb) Multiome | 333 | |
| chr12:48,814,087–48,815,981 | 204.1 kb | Distal (>10kb) Multiome | 815 | |
| chr12:48,817,927–48,819,273 | 200.3 kb | Distal (>10kb) Multiome | 459 | |
| chr12:48,851,862–48,852,825 | 166.7 kb | Distal (>10kb) Multiome | 900 | |
| chr12:48,864,974–48,866,292 | 153.0 kb | Distal (>10kb) Multiome | 649 | |
| chr12:48,883,231–48,884,168 | 135.1 kb | Distal (>10kb) Multiome | 433 | |
| chr12:48,890,671–48,891,380 | 127.9 kb | Distal (>10kb) Multiome | 517 | |
| chr12:48,924,659–48,925,688 | 94.0 kb | Distal (>10kb) Multiome | 413 | |
| chr12:48,956,252–48,957,974 | 62.4 kb | Distal (>10kb) Multiome | 831 | |
| chr12:48,978,055–48,978,819 | 40.6 kb | Distal (>10kb) Multiome | 360 | |
| chr12:48,980,647–48,981,153 | 38.0 kb | Distal (>10kb) Multiome | 259 | |
| chr12:48,988,160–48,988,373 | 10.0 kb | Proximal (<10kb) | 177 | |
| chr12:48,995,444–48,995,718 | 2.6 kb | Proximal (<10kb) | 330 | |
| chr12:48,996,820–48,997,211 | 1.2 kb | Proximal (<10kb) | 303 | |
| chr12:48,997,612–48,998,829 | 20.6 kb | Distal (>10kb) Multiome HiCAR | 620 | |
| chr12:49,018,007–49,019,184 | 160 bp | At TSS Multiome | 899 | |
| chr12:49,059,883–49,061,347 | 41.9 kb | Distal (>10kb) Multiome | 1060 | |
| chr12:49,069,381–49,070,589 | 51.1 kb | Distal (>10kb) Multiome | 804 | |
| chr12:49,088,153–49,088,744 | 69.6 kb | Distal (>10kb) Multiome | 473 | |
| chr12:49,109,990–49,111,248 | 92.0 kb | Distal (>10kb) Multiome | 693 | |
| chr12:49,129,851–49,132,062 | 111.5 kb | Distal (>10kb) Multiome | 1233 | |
| chr12:49,188,266–49,189,371 | 170.2 kb | Distal (>10kb) Multiome | 676 | |
| chr12:49,228,702–49,229,259 | 210.0 kb | Distal (>10kb) Multiome | 64 | |
| chr12:49,234,459–49,235,140 | 215.8 kb | Distal (>10kb) Multiome | 786 | |
| chr12:49,264,393–49,265,769 | 246.1 kb | Distal (>10kb) Multiome | 1032 |
Genomic view of the DDN-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.