Transcription factors with Perturb-seq knockdown data for SNHG4. 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 = SNHG4 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 SNHG4, 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 |
|---|---|---|---|---|
| chr5:138,463,424–138,467,199 | 810.0 kb | Distal (>10kb) Multiome HiCAR | 1117 | |
| chr5:138,574,967–138,576,411 | 698.4 kb | Distal (>10kb) Multiome HiCAR | 1066 | |
| chr5:138,962,635–138,963,294 | 311.2 kb | Distal (>10kb) Multiome HiCAR | 35 | |
| chr5:138,998,417–138,998,944 | 275.4 kb | Distal (>10kb) Multiome | 46 | |
| chr5:139,197,672–139,198,627 | 75.7 kb | Distal (>10kb) Multiome | 851 | |
| chr5:139,273,424–139,274,448 | 68 bp | At TSS Multiome | 843 | |
| chr5:139,277,192–139,277,580 | 3.1 kb | Proximal (<10kb) | 50 | |
| chr5:139,278,542–139,279,114 | 4.4 kb | Proximal (<10kb) | 59 | |
| chr5:139,283,068–139,284,092 | 9.6 kb | Proximal (<10kb) Multiome | 194 | |
| chr5:139,293,312–139,294,807 | 19.6 kb | Distal (>10kb) Multiome | 994 | |
| chr5:139,341,351–139,342,686 | 67.7 kb | Distal (>10kb) Multiome | 1002 | |
| chr5:139,378,115–139,378,885 | 104.3 kb | Distal (>10kb) Multiome | 122 | |
| chr5:139,391,978–139,393,556 | 118.6 kb | Distal (>10kb) Multiome | 424 | |
| chr5:139,396,045–139,397,275 | 122.8 kb | Distal (>10kb) Multiome | 134 | |
| chr5:139,403,383–139,404,694 | 129.9 kb | Distal (>10kb) Multiome | 772 | |
| chr5:139,438,861–139,439,913 | 165.3 kb | Distal (>10kb) Multiome | 726 | |
| chr5:139,517,739–139,518,561 | 244.0 kb | Distal (>10kb) Multiome | 1046 | |
| chr5:139,523,548–139,524,678 | 250.1 kb | Distal (>10kb) Multiome | 320 | |
| chr5:139,560,824–139,562,261 | 287.2 kb | Distal (>10kb) Multiome | 970 |
Genomic view of the SNHG4 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.