Transcription factors with Perturb-seq knockdown data for CLHC1. 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 = CLHC1 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 CLHC1, 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 |
|---|---|---|---|---|
| chr2:54,945,613–54,946,419 | 286.1 kb | Distal (>10kb) Multiome | 135 | |
| chr2:55,048,854–55,051,460 | 181.5 kb | Distal (>10kb) Multiome | 1172 | |
| chr2:55,133,866–55,134,461 | 98.1 kb | Distal (>10kb) Multiome | 417 | |
| chr2:55,223,149–55,223,979 | 8.5 kb | Proximal (<10kb) Multiome | 386 | |
| chr2:55,231,636–55,233,143 | 230 bp | At TSS Multiome | 993 | |
| chr2:55,268,856–55,269,481 | 37.1 kb | Distal (>10kb) Multiome | 1083 | |
| chr2:55,279,327–55,280,579 | 47.6 kb | Distal (>10kb) Multiome | 219 | |
| chr2:55,281,727–55,282,873 | 50.1 kb | Distal (>10kb) Multiome | 943 | |
| chr2:55,418,822–55,420,474 | 187.8 kb | Distal (>10kb) Multiome | 1181 | |
| chr2:55,518,709–55,520,527 | 287.4 kb | Distal (>10kb) Multiome | 882 |
Genomic view of the CLHC1 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.