Transcription factors with Perturb-seq knockdown data for LIMD1-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 = LIMD1-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 LIMD1-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 |
|---|---|---|---|---|
| chr3:45,593,037–45,594,632 | 95.8 kb | Distal (>10kb) Multiome | 938 | |
| chr3:45,673,142–45,673,693 | 15.8 kb | Distal (>10kb) Multiome | 31 | |
| chr3:45,684,209–45,684,875 | 4.6 kb | Proximal (<10kb) Multiome | 109 | |
| chr3:45,685,643–45,686,405 | 3.1 kb | Proximal (<10kb) Multiome | 42 | |
| chr3:45,688,221–45,689,801 | 44 bp | At TSS Multiome | 1010 | |
| chr3:45,756,823–45,757,497 | 68.2 kb | Distal (>10kb) Multiome | 7 | |
| chr3:45,760,846–45,761,421 | 72.0 kb | Distal (>10kb) Multiome | 280 | |
| chr3:45,796,192–45,796,864 | 107.3 kb | Distal (>10kb) Multiome | 188 | |
| chr3:45,841,672–45,842,368 | 153.0 kb | Distal (>10kb) Multiome | 746 |
Genomic view of the LIMD1-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.