Transcription factors with Perturb-seq knockdown data for CCDC28A-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 = CCDC28A-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 CCDC28A-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 |
|---|---|---|---|---|
| chr6:138,485,936–138,486,779 | 287.1 kb | Distal (>10kb) Multiome | 199 | |
| chr6:138,691,712–138,693,955 | 80.1 kb | Distal (>10kb) Multiome | 807 | |
| chr6:138,772,879–138,774,086 | 180 bp | At TSS Multiome | 833 | |
| chr6:138,795,674–138,796,576 | 22.7 kb | Distal (>10kb) Multiome | 181 | |
| chr6:138,817,772–138,818,464 | 44.7 kb | Distal (>10kb) Multiome | 321 | |
| chr6:138,890,955–138,892,013 | 118.0 kb | Distal (>10kb) Multiome | 99 | |
| chr6:138,987,166–138,988,932 | 214.8 kb | Distal (>10kb) Multiome | 1012 | |
| chr6:139,010,370–139,011,354 | 237.5 kb | Distal (>10kb) Multiome | 168 | |
| chr6:139,028,353–139,030,017 | 255.3 kb | Distal (>10kb) Multiome | 798 |
Genomic view of the CCDC28A-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.