Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for SNHG3. 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 = SNHG3 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 SNHG3, 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 |
|---|---|---|---|---|
| chr1:28,232,593–28,233,160 | 273.0 kb | Distal (>10kb) Multiome | 666 | |
| chr1:28,235,692–28,236,588 | 270.0 kb | Distal (>10kb) Multiome | 862 | |
| chr1:28,247,126–28,247,685 | 258.7 kb | Distal (>10kb) Multiome | 544 | |
| chr1:28,258,840–28,260,822 | 245.6 kb | Distal (>10kb) Multiome HiCAR | 910 | |
| chr1:28,369,387–28,370,499 | 136.3 kb | Distal (>10kb) Multiome | 961 | |
| chr1:28,505,412–28,506,885 | 93 bp | At TSS Multiome | 969 | |
| chr1:28,507,602–28,508,074 | 1.6 kb | Proximal (<10kb) | 236 | |
| chr1:28,508,380–28,508,689 | 2.3 kb | Proximal (<10kb) | 222 | |
| chr1:28,510,330–28,511,247 | 4.3 kb | Proximal (<10kb) | 617 | |
| chr1:28,511,458–28,511,980 | 5.4 kb | Proximal (<10kb) | 217 | |
| chr1:28,513,136–28,516,505 | 9.5 kb | Proximal (<10kb) Multiome | 461 | |
| chr1:28,517,302–28,519,364 | 12.3 kb | Distal (>10kb) Multiome | 927 | |
| chr1:28,552,370–28,553,806 | 46.9 kb | Distal (>10kb) Multiome | 955 | |
| chr1:28,580,985–28,582,501 | 75.8 kb | Distal (>10kb) Multiome | 1080 | |
| chr1:28,592,018–28,592,768 | 86.4 kb | Distal (>10kb) Multiome | 394 | |
| chr1:28,642,403–28,643,726 | 137.1 kb | Distal (>10kb) Multiome | 980 | |
| chr1:28,648,003–28,650,002 | 142.8 kb | Distal (>10kb) Multiome | 1377 | |
| chr1:28,667,742–28,669,783 | 162.4 kb | Distal (>10kb) Multiome | 804 | |
| chr1:28,736,098–28,738,080 | 230.7 kb | Distal (>10kb) Multiome | 1106 |
Genomic view of the SNHG3 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.