Transcription factors with Perturb-seq knockdown data for FOXD3-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 = FOXD3-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 FOXD3-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 |
|---|---|---|---|---|
| chr1:63,189,665–63,190,489 | 132.3 kb | Distal (>10kb) Multiome | 215 | |
| chr1:63,198,425–63,199,296 | 123.7 kb | Distal (>10kb) Multiome | 65 | |
| chr1:63,316,605–63,317,949 | 5.2 kb | Proximal (<10kb) Multiome | 584 | |
| chr1:63,319,478–63,320,003 | 1.7 kb | Proximal (<10kb) | 118 | |
| chr1:63,320,118–63,320,808 | 856 bp | At TSS | 76 | |
| chr1:63,321,080–63,321,448 | 216 bp | At TSS | 51 | |
| chr1:63,321,551–63,321,712 | at TSS | At TSS | 44 | |
| chr1:63,321,880–63,324,736 | 22 bp | At TSS Multiome | 684 | |
| chr1:63,326,144–63,327,160 | 3.9 kb | Proximal (<10kb) Multiome | 213 | |
| chr1:63,327,552–63,328,285 | 5.3 kb | Proximal (<10kb) Multiome | 328 | |
| chr1:63,329,526–63,330,869 | 8.2 kb | Proximal (<10kb) Multiome | 128 | |
| chr1:63,367,059–63,368,178 | 45.1 kb | Distal (>10kb) Multiome | 818 | |
| chr1:63,522,907–63,524,033 | 200.9 kb | Distal (>10kb) Multiome | 1049 | |
| chr1:63,574,025–63,574,937 | 252.1 kb | Distal (>10kb) Multiome | 44 | |
| chr1:63,592,855–63,594,596 | 271.0 kb | Distal (>10kb) Multiome | 842 | |
| chr1:63,613,061–63,613,814 | 290.8 kb | Distal (>10kb) Multiome | 42 |
Genomic view of the FOXD3-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.