Transcription factors with Perturb-seq knockdown data for CHROMR. 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 = CHROMR 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 CHROMR, 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 |
|---|---|---|---|---|
| chr2:178,112,051–178,113,183 | 301.2 kb | Distal (>10kb) Multiome HiCAR | 1042 | |
| chr2:178,193,538–178,195,689 | 219.3 kb | Distal (>10kb) Multiome | 876 | |
| chr2:178,211,552–178,212,360 | 201.6 kb | Distal (>10kb) Multiome | 170 | |
| chr2:178,413,219–178,414,399 | 56 bp | At TSS Multiome | 734 | |
| chr2:178,414,525–178,415,185 | 1.3 kb | Proximal (<10kb) Multiome | 748 | |
| chr2:178,450,146–178,452,280 | 37.5 kb | Distal (>10kb) Multiome | 1097 | |
| chr2:178,477,968–178,479,684 | 65.2 kb | Distal (>10kb) Multiome | 943 | |
| chr2:178,479,849–178,481,204 | 66.8 kb | Distal (>10kb) Multiome | 786 | |
| chr2:178,522,788–178,524,094 | 109.5 kb | Distal (>10kb) Multiome | 612 |
Genomic view of the CHROMR 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.