This locus represents a small nucleolar RNA host gene that produces multiple alternatively spliced long non-coding RNAs. This gene is upregulated in cancers and is thought to act as promoter of cell proliferation. This transcript negatively regulates tumor suppressor genes such as tumor protein p53. Expression of this locus may be a marker of tumor progression. [provided by RefSeq, Dec 2017]
Transcription factors with Perturb-seq knockdown data for SNHG1. 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 = SNHG1 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 SNHG1, 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 |
|---|---|---|---|---|
| chr11:62,555,905–62,556,742 | 299.7 kb | Distal (>10kb) Multiome | 545 | |
| chr11:62,560,588–62,561,104 | 295.3 kb | Distal (>10kb) Multiome | 541 | |
| chr11:62,561,760–62,562,358 | 293.9 kb | Distal (>10kb) Multiome | 43 | |
| chr11:62,573,347–62,574,645 | 281.9 kb | Distal (>10kb) Multiome | 845 | |
| chr11:62,591,246–62,592,462 | 264.2 kb | Distal (>10kb) Multiome | 976 | |
| chr11:62,600,988–62,603,291 | 254.0 kb | Distal (>10kb) Multiome | 872 | |
| chr11:62,611,665–62,613,544 | 243.1 kb | Distal (>10kb) Multiome | 737 | |
| chr11:62,621,550–62,622,445 | 233.9 kb | Distal (>10kb) Multiome | 964 | |
| chr11:62,646,025–62,647,031 | 209.3 kb | Distal (>10kb) Multiome | 815 | |
| chr11:62,652,836–62,653,744 | 202.6 kb | Distal (>10kb) Multiome | 921 | |
| chr11:62,664,567–62,666,291 | 190.7 kb | Distal (>10kb) Multiome | 1020 | |
| chr11:62,671,328–62,672,522 | 184.2 kb | Distal (>10kb) Multiome | 882 | |
| chr11:62,705,543–62,707,930 | 149.6 kb | Distal (>10kb) Multiome | 760 | |
| chr11:62,708,691–62,710,293 | 146.3 kb | Distal (>10kb) Multiome | 531 | |
| chr11:62,726,557–62,728,947 | 128.3 kb | Distal (>10kb) Multiome | 1088 | |
| chr11:62,753,347–62,754,665 | 101.8 kb | Distal (>10kb) Multiome | 696 | |
| chr11:62,761,085–62,762,045 | 94.5 kb | Distal (>10kb) Multiome | 649 | |
| chr11:62,770,753–62,772,068 | 84.5 kb | Distal (>10kb) Multiome | 885 | |
| chr11:62,786,365–62,787,860 | 69.4 kb | Distal (>10kb) Multiome | 1073 | |
| chr11:62,791,569–62,792,385 | 63.9 kb | Distal (>10kb) Multiome | 805 | |
| chr11:62,804,451–62,807,080 | 50.4 kb | Distal (>10kb) Multiome | 994 | |
| chr11:62,831,037–62,832,904 | 24.0 kb | Distal (>10kb) Multiome | 870 | |
| chr11:62,839,042–62,842,743 | 14.6 kb | Distal (>10kb) Multiome | 1403 | |
| chr11:62,850,412–62,850,747 | 5.2 kb | Proximal (<10kb) | 137 | |
| chr11:62,851,028–62,851,955 | 4.5 kb | Proximal (<10kb) Multiome | 421 | |
| chr11:62,855,209–62,856,560 | 45 bp | At TSS Multiome | 1071 | |
| chr11:62,862,252–62,862,948 | 6.8 kb | Proximal (<10kb) Multiome | 360 | |
| chr11:62,880,343–62,881,977 | 24.9 kb | Distal (>10kb) Multiome | 1080 | |
| chr11:62,909,033–62,909,985 | 53.4 kb | Distal (>10kb) Multiome | 366 |
Genomic view of the SNHG1 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.