Transcription factors with Perturb-seq knockdown data for LNP1. 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 = LNP1 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 LNP1, 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 |
|---|---|---|---|---|
| chr3:100,260,138–100,261,732 | 140.7 kb | Distal (>10kb) Multiome | 908 | |
| chr3:100,334,205–100,335,290 | 66.8 kb | Distal (>10kb) Multiome | 849 | |
| chr3:100,400,431–100,402,077 | 210 bp | At TSS Multiome | 977 | |
| chr3:100,403,404–100,403,783 | 1.9 kb | Proximal (<10kb) | 113 | |
| chr3:100,491,845–100,493,045 | 90.9 kb | Distal (>10kb) Multiome | 816 | |
| chr3:100,601,812–100,603,934 | 200.9 kb | Distal (>10kb) Multiome | 474 |
Genomic view of the LNP1 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.