Transcription factors with Perturb-seq knockdown data for CXXC4-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 = CXXC4-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 CXXC4-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 |
|---|---|---|---|---|
| chr4:104,490,489–104,492,982 | at TSS | At TSS | 671 | |
| chr4:104,493,172–104,494,092 | 2.2 kb | Proximal (<10kb) | 96 | |
| chr4:104,494,466–104,495,681 | 3.5 kb | Proximal (<10kb) | 566 | |
| chr4:104,498,072–104,498,557 | 7.1 kb | Proximal (<10kb) | 7 | |
| chr4:104,499,615–104,499,867 | 8.7 kb | Proximal (<10kb) | 13 | |
| chr4:104,500,026–104,500,709 | 9.1 kb | Proximal (<10kb) | 28 |
Genomic view of the CXXC4-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.