Transcription factors with Perturb-seq knockdown data for LIM2-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 = LIM2-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 LIM2-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 |
|---|---|---|---|---|
| chr19:51,107,794–51,109,056 | 286.1 kb | Distal (>10kb) Multiome | 750 | |
| chr19:51,311,132–51,312,279 | 82.9 kb | Distal (>10kb) Multiome | 99 | |
| chr19:51,327,535–51,328,038 | 66.6 kb | Distal (>10kb) Multiome | 288 | |
| chr19:51,338,815–51,340,814 | 55.5 kb | Distal (>10kb) Multiome | 827 | |
| chr19:51,365,646–51,368,695 | 26.7 kb | Distal (>10kb) Multiome | 1057 | |
| chr19:51,390,425–51,391,164 | 3.8 kb | Proximal (<10kb) Multiome | 171 | |
| chr19:51,393,803–51,394,830 | 91 bp | At TSS Multiome | 725 | |
| chr19:51,421,811–51,422,246 | 27.6 kb | Distal (>10kb) Multiome | 848 | |
| chr19:51,593,934–51,594,889 | 200.0 kb | Distal (>10kb) Multiome | 581 | |
| chr19:51,687,813–51,691,477 | 296.6 kb | Distal (>10kb) Multiome | 820 |
Genomic view of the LIM2-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.