Transcription factors with Perturb-seq knockdown data for SCIRT. 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 = SCIRT 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 SCIRT, 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 |
|---|---|---|---|---|
| chr6:43,575,269–43,576,483 | 498.6 kb | Distal (>10kb) Multiome HiCAR | 1044 | |
| chr6:43,628,488–43,630,447 | 444.5 kb | Distal (>10kb) Multiome HiCAR | 1157 | |
| chr6:43,635,496–43,636,104 | 438.8 kb | Distal (>10kb) Multiome HiCAR | 941 | |
| chr6:43,644,712–43,645,902 | 429.3 kb | Distal (>10kb) Multiome HiCAR | 255 | |
| chr6:43,667,273–43,667,900 | 407.3 kb | Distal (>10kb) Multiome HiCAR | 625 | |
| chr6:43,667,997–43,668,873 | 406.2 kb | Distal (>10kb) Multiome HiCAR | 664 | |
| chr6:43,702,335–43,703,403 | 371.7 kb | Distal (>10kb) Multiome HiCAR | 713 | |
| chr6:43,706,840–43,708,370 | 366.7 kb | Distal (>10kb) Multiome HiCAR | 307 | |
| chr6:43,739,421–43,740,065 | 334.9 kb | Distal (>10kb) Multiome HiCAR | 175 | |
| chr6:43,769,188–43,772,162 | 304.7 kb | Distal (>10kb) Multiome HiCAR | 1112 | |
| chr6:43,926,273–43,928,465 | 147.4 kb | Distal (>10kb) Multiome HiCAR | 1000 | |
| chr6:43,951,107–43,951,921 | 123.2 kb | Distal (>10kb) Multiome HiCAR | 591 | |
| chr6:44,002,061–44,003,708 | 71.9 kb | Distal (>10kb) Multiome HiCAR | 581 | |
| chr6:44,126,767–44,128,943 | 52.8 kb | Distal (>10kb) Multiome | 845 | |
| chr6:44,151,741–44,152,312 | 77.4 kb | Distal (>10kb) Multiome | 575 | |
| chr6:44,185,920–44,186,571 | 111.6 kb | Distal (>10kb) Multiome | 95 | |
| chr6:44,202,490–44,203,242 | 128.2 kb | Distal (>10kb) Multiome | 229 | |
| chr6:44,218,945–44,220,120 | 144.9 kb | Distal (>10kb) Multiome | 799 | |
| chr6:44,223,166–44,224,465 | 149.0 kb | Distal (>10kb) Multiome | 783 | |
| chr6:44,234,203–44,235,350 | 160.2 kb | Distal (>10kb) Multiome | 499 | |
| chr6:44,237,380–44,238,386 | 163.3 kb | Distal (>10kb) Multiome | 969 | |
| chr6:44,245,610–44,248,192 | 173.3 kb | Distal (>10kb) Multiome | 1271 | |
| chr6:44,256,209–44,258,064 | 182.8 kb | Distal (>10kb) Multiome | 1042 | |
| chr6:44,264,892–44,265,788 | 190.9 kb | Distal (>10kb) Multiome | 760 | |
| chr6:44,270,373–44,271,349 | 196.4 kb | Distal (>10kb) Multiome | 166 | |
| chr6:44,297,234–44,298,035 | 223.1 kb | Distal (>10kb) Multiome | 356 | |
| chr6:44,312,866–44,313,523 | 238.6 kb | Distal (>10kb) Multiome | 1073 |
Genomic view of the SCIRT 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.