Transcription factors with Perturb-seq knockdown data for FOXD2-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 = FOXD2-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 FOXD2-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 |
|---|---|---|---|---|
| chr1:47,424,446–47,424,949 | 9.7 kb | Proximal (<10kb) | 274 | |
| chr1:47,431,307–47,431,881 | 2.8 kb | Proximal (<10kb) | 90 | |
| chr1:47,432,258–47,433,058 | 1.6 kb | Proximal (<10kb) | 298 | |
| chr1:47,436,505–47,439,686 | 1.9 kb | Proximal (<10kb) | 844 | |
| chr1:47,444,077–47,444,297 | 9.4 kb | Proximal (<10kb) | 40 |
Genomic view of the FOXD2-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.