Transcription factors with Perturb-seq knockdown data for HMGA1P4. 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 = HMGA1P4 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 HMGA1P4, 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 |
|---|---|---|---|---|
| chr9:128,420,259–128,421,260 | 263.8 kb | Distal (>10kb) Multiome | 701 | |
| chr9:128,455,721–128,456,522 | 228.4 kb | Distal (>10kb) Multiome | 684 | |
| chr9:128,504,482–128,505,188 | 179.8 kb | Distal (>10kb) Multiome | 766 | |
| chr9:128,552,006–128,553,125 | 132.0 kb | Distal (>10kb) Multiome | 839 | |
| chr9:128,656,436–128,657,126 | 27.7 kb | Distal (>10kb) Multiome | 1009 | |
| chr9:128,683,393–128,684,010 | 861 bp | At TSS Multiome | 296 | |
| chr9:128,684,170–128,684,813 | 239 bp | At TSS Multiome | 574 | |
| chr9:128,688,449–128,689,713 | 4.6 kb | Proximal (<10kb) Multiome | 805 | |
| chr9:128,702,246–128,702,946 | 18.1 kb | Distal (>10kb) Multiome | 720 | |
| chr9:128,723,691–128,725,229 | 39.7 kb | Distal (>10kb) Multiome | 821 | |
| chr9:128,771,658–128,772,301 | 87.5 kb | Distal (>10kb) Multiome | 940 | |
| chr9:128,786,928–128,787,516 | 102.7 kb | Distal (>10kb) Multiome | 1040 | |
| chr9:128,818,208–128,819,406 | 134.0 kb | Distal (>10kb) Multiome | 839 | |
| chr9:128,829,505–128,830,189 | 145.3 kb | Distal (>10kb) Multiome | 782 | |
| chr9:128,881,863–128,882,454 | 197.6 kb | Distal (>10kb) Multiome | 777 | |
| chr9:128,921,941–128,922,727 | 237.8 kb | Distal (>10kb) Multiome | 378 | |
| chr9:128,947,329–128,947,815 | 263.1 kb | Distal (>10kb) Multiome | 865 |
Genomic view of the HMGA1P4 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.