Transcription factors with Perturb-seq knockdown data for CISTR. 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 = CISTR 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 CISTR, 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 |
|---|---|---|---|---|
| chr12:53,492,147–53,494,149 | 264.1 kb | Distal (>10kb) Multiome | 702 | |
| chr12:53,498,714–53,500,111 | 257.8 kb | Distal (>10kb) Multiome | 454 | |
| chr12:53,500,242–53,501,839 | 256.2 kb | Distal (>10kb) Multiome | 1010 | |
| chr12:53,625,664–53,626,787 | 131.0 kb | Distal (>10kb) Multiome | 880 | |
| chr12:53,675,553–53,677,839 | 81.1 kb | Distal (>10kb) Multiome | 1104 | |
| chr12:53,696,162–53,696,648 | 60.7 kb | Distal (>10kb) Multiome HiCAR | 228 | |
| chr12:53,727,002–53,728,055 | 29.6 kb | Distal (>10kb) Multiome | 768 | |
| chr12:53,738,393–53,738,964 | 18.5 kb | Distal (>10kb) Multiome | 131 | |
| chr12:53,746,454–53,746,954 | 10.4 kb | Distal (>10kb) Multiome | 503 | |
| chr12:53,756,873–53,757,721 | 50 bp | At TSS Multiome | 367 | |
| chr12:53,938,348–53,939,947 | 181.4 kb | Distal (>10kb) Multiome | 537 | |
| chr12:53,984,667–53,985,381 | 227.8 kb | Distal (>10kb) Multiome | 456 | |
| chr12:54,017,619–54,018,921 | 260.8 kb | Distal (>10kb) Multiome | 663 |
Genomic view of the CISTR 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.