Transcription factors with Perturb-seq knockdown data for GBX2-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 = GBX2-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 GBX2-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 |
|---|---|---|---|---|
| chr2:236,086,912–236,087,522 | 80.3 kb | Distal (>10kb) Multiome | 92 | |
| chr2:236,159,024–236,160,074 | 7.9 kb | Proximal (<10kb) Multiome | 207 | |
| chr2:236,160,792–236,161,258 | 6.2 kb | Proximal (<10kb) | 66 | |
| chr2:236,163,152–236,165,145 | 2.8 kb | Proximal (<10kb) Multiome | 243 | |
| chr2:236,166,188–236,166,513 | 950 bp | At TSS | 70 | |
| chr2:236,167,071–236,169,001 | 1.1 kb | Proximal (<10kb) Multiome | 531 | |
| chr2:236,172,801–236,174,041 | 5.3 kb | Proximal (<10kb) | 141 | |
| chr2:236,174,344–236,174,963 | 6.9 kb | Proximal (<10kb) | 27 | |
| chr2:236,177,631–236,178,437 | 10.7 kb | Distal (>10kb) Multiome | 437 | |
| chr2:236,237,432–236,238,127 | 70.3 kb | Distal (>10kb) Multiome | 130 |
Genomic view of the GBX2-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.