Transcription factors with Perturb-seq knockdown data for KDM4A-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 = KDM4A-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 KDM4A-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 |
|---|---|---|---|---|
| chr1:43,452,851–43,454,257 | 254.0 kb | Distal (>10kb) Multiome | 455 | |
| chr1:43,454,433–43,454,997 | 252.7 kb | Distal (>10kb) Multiome | 267 | |
| chr1:43,530,512–43,532,007 | 176.4 kb | Distal (>10kb) Multiome | 520 | |
| chr1:43,545,657–43,546,353 | 161.4 kb | Distal (>10kb) Multiome | 445 | |
| chr1:43,549,934–43,550,659 | 157.1 kb | Distal (>10kb) Multiome | 343 | |
| chr1:43,565,502–43,566,158 | 141.6 kb | Distal (>10kb) Multiome | 173 | |
| chr1:43,649,463–43,650,795 | 57.2 kb | Distal (>10kb) Multiome | 997 | |
| chr1:43,707,108–43,708,162 | 168 bp | At TSS Multiome | 937 | |
| chr1:43,933,385–43,935,511 | 227.6 kb | Distal (>10kb) Multiome HiCAR | 565 | |
| chr1:43,935,659–43,937,001 | 229.3 kb | Distal (>10kb) Multiome HiCAR | 359 | |
| chr1:43,946,199–43,947,337 | 239.3 kb | Distal (>10kb) Multiome | 1003 | |
| chr1:43,969,717–43,970,284 | 262.5 kb | Distal (>10kb) Multiome | 515 | |
| chr1:43,974,246–43,975,571 | 267.5 kb | Distal (>10kb) Multiome | 875 | |
| chr1:43,978,661–43,979,381 | 271.7 kb | Distal (>10kb) Multiome | 419 | |
| chr1:43,991,242–43,992,448 | 284.5 kb | Distal (>10kb) Multiome | 780 | |
| chr1:44,000,140–44,000,654 | 293.1 kb | Distal (>10kb) Multiome | 43 |
Genomic view of the KDM4A-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.