Transcription factors with Perturb-seq knockdown data for GCC2-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 = GCC2-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 GCC2-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 |
|---|---|---|---|---|
| chr2:108,403,524–108,403,993 | 130.4 kb | Distal (>10kb) Multiome | 154 | |
| chr2:108,448,417–108,449,710 | 85.1 kb | Distal (>10kb) Multiome | 999 | |
| chr2:108,531,069–108,531,657 | 2.5 kb | Proximal (<10kb) | 48 | |
| chr2:108,533,404–108,535,229 | 71 bp | At TSS Multiome | 1035 | |
| chr2:108,583,732–108,584,281 | 49.9 kb | Distal (>10kb) Multiome | 283 | |
| chr2:108,608,990–108,609,565 | 75.2 kb | Distal (>10kb) Multiome | 125 | |
| chr2:108,620,806–108,621,587 | 87.0 kb | Distal (>10kb) Multiome | 401 | |
| chr2:108,636,177–108,636,884 | 102.3 kb | Distal (>10kb) Multiome | 398 | |
| chr2:108,718,922–108,720,037 | 185.3 kb | Distal (>10kb) Multiome | 1042 | |
| chr2:108,786,273–108,787,203 | 252.6 kb | Distal (>10kb) Multiome | 874 |
Genomic view of the GCC2-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.