Transcription factors with Perturb-seq knockdown data for CCDC71. 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 = CCDC71 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 CCDC71, 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 |
|---|---|---|---|---|
| chr3:48,898,423–48,899,110 | 267.4 kb | Distal (>10kb) Multiome | 739 | |
| chr3:48,918,234–48,919,609 | 247.5 kb | Distal (>10kb) Multiome | 877 | |
| chr3:48,989,537–48,991,069 | 176.3 kb | Distal (>10kb) Multiome | 552 | |
| chr3:49,003,975–49,004,995 | 161.8 kb | Distal (>10kb) Multiome | 209 | |
| chr3:49,006,738–49,008,496 | 158.4 kb | Distal (>10kb) Multiome | 955 | |
| chr3:49,017,789–49,018,870 | 147.9 kb | Distal (>10kb) Multiome | 780 | |
| chr3:49,020,066–49,022,597 | 144.6 kb | Distal (>10kb) Multiome | 1064 | |
| chr3:49,028,856–49,029,800 | 136.9 kb | Distal (>10kb) Multiome | 974 | |
| chr3:49,093,005–49,094,956 | 72.0 kb | Distal (>10kb) Multiome | 944 | |
| chr3:49,104,279–49,105,309 | 61.6 kb | Distal (>10kb) Multiome | 712 | |
| chr3:49,120,575–49,121,282 | 45.4 kb | Distal (>10kb) Multiome | 765 | |
| chr3:49,132,603–49,133,965 | 32.6 kb | Distal (>10kb) Multiome | 652 | |
| chr3:49,166,057–49,166,586 | 2 bp | At TSS Multiome | 622 | |
| chr3:49,170,896–49,171,950 | 5.0 kb | Proximal (<10kb) Multiome | 781 | |
| chr3:49,173,433–49,173,695 | 7.1 kb | Proximal (<10kb) | 160 | |
| chr3:49,276,912–49,277,398 | 110.7 kb | Distal (>10kb) Multiome | 291 | |
| chr3:49,339,607–49,340,853 | 173.9 kb | Distal (>10kb) Multiome | 1044 | |
| chr3:49,357,868–49,359,083 | 192.1 kb | Distal (>10kb) Multiome | 908 | |
| chr3:49,411,409–49,412,844 | 245.8 kb | Distal (>10kb) Multiome | 899 | |
| chr3:49,422,179–49,422,905 | 256.2 kb | Distal (>10kb) Multiome HiCAR | 453 | |
| chr3:49,428,857–49,429,869 | 263.1 kb | Distal (>10kb) Multiome HiCAR | 712 | |
| chr3:49,461,484–49,462,134 | 295.4 kb | Distal (>10kb) Multiome | 207 | |
| chr3:49,468,926–49,470,930 | 303.9 kb | Distal (>10kb) Multiome HiCAR | 919 |
Genomic view of the CCDC71 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.