Transcription factors with Perturb-seq knockdown data for DIRC3. 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 = DIRC3 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 DIRC3, 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 |
|---|---|---|---|---|
| chr2:216,498,326–216,499,289 | 935.4 kb | Distal (>10kb) Multiome HiCAR | 982 | |
| chr2:216,606,380–216,607,387 | 827.4 kb | Distal (>10kb) Multiome HiCAR | 243 | |
| chr2:216,619,507–216,620,419 | 814.3 kb | Distal (>10kb) Multiome HiCAR | 382 | |
| chr2:216,632,597–216,634,235 | 800.9 kb | Distal (>10kb) Multiome HiCAR | 459 | |
| chr2:216,635,691–216,637,041 | 797.4 kb | Distal (>10kb) Multiome HiCAR | 263 | |
| chr2:216,665,266–216,666,969 | 768.5 kb | Distal (>10kb) Multiome HiCAR | 454 | |
| chr2:216,691,972–216,693,060 | 742.0 kb | Distal (>10kb) Multiome HiCAR | 383 | |
| chr2:216,694,105–216,695,084 | 739.7 kb | Distal (>10kb) Multiome HiCAR | 316 | |
| chr2:216,695,439–216,696,027 | 738.5 kb | Distal (>10kb) Multiome HiCAR | 258 | |
| chr2:216,765,712–216,766,366 | 668.2 kb | Distal (>10kb) Multiome HiCAR | 240 | |
| chr2:216,777,662–216,778,166 | 656.4 kb | Distal (>10kb) Multiome HiCAR | 399 | |
| chr2:217,147,664–217,148,672 | 286.2 kb | Distal (>10kb) Multiome HiCAR | 179 | |
| chr2:217,149,147–217,149,754 | 284.7 kb | Distal (>10kb) Multiome HiCAR | 75 | |
| chr2:217,209,492–217,210,153 | 224.6 kb | Distal (>10kb) Multiome | 53 | |
| chr2:217,269,729–217,270,938 | 163.9 kb | Distal (>10kb) Multiome | 194 | |
| chr2:217,289,303–217,290,328 | 144.4 kb | Distal (>10kb) Multiome | 292 | |
| chr2:217,386,202–217,387,041 | 47.5 kb | Distal (>10kb) Multiome | 85 | |
| chr2:217,433,581–217,433,887 | 328 bp | At TSS | 49 | |
| chr2:217,434,150–217,434,638 | 68 bp | At TSS Multiome HiCAR | 238 | |
| chr2:217,621,957–217,623,171 | 188.1 kb | Distal (>10kb) Multiome | 391 | |
| chr2:217,756,309–217,757,077 | 322.5 kb | Distal (>10kb) Multiome HiCAR | 391 | |
| chr2:217,943,677–217,944,438 | 509.9 kb | Distal (>10kb) Multiome | 486 | |
| chr2:217,978,332–217,979,228 | 544.5 kb | Distal (>10kb) Multiome | 246 | |
| chr2:217,987,861–217,989,008 | 554.2 kb | Distal (>10kb) Multiome | 528 | |
| chr2:218,033,728–218,035,208 | 600.7 kb | Distal (>10kb) Multiome | 270 |
Genomic view of the DIRC3 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.