This gene encodes a member of a family of proteins that contain a methyl-CpG-binding domain (MBD) and a SET domain and function as histone methyltransferases. This protein is recruited to heterochromatin and plays a role in the regulation of chromosome segregation. This region is commonly deleted in chronic lymphocytic leukemia. Naturally-occuring readthrough transcription occurs from this gene to the downstream PHF11 (PHD finger protein 11) gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
Transcription factors with Perturb-seq knockdown data for SETDB2. 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 = SETDB2 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 SETDB2, 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 |
|---|---|---|---|---|
| chr13:49,184,188–49,185,149 | 259.5 kb | Distal (>10kb) Multiome | 84 | |
| chr13:49,218,368–49,219,071 | 225.5 kb | Distal (>10kb) Multiome | 51 | |
| chr13:49,219,748–49,221,361 | 224.0 kb | Distal (>10kb) Multiome | 441 | |
| chr13:49,247,525–49,248,779 | 196.3 kb | Distal (>10kb) Multiome | 752 | |
| chr13:49,280,990–49,281,662 | 163.0 kb | Distal (>10kb) Multiome | 111 | |
| chr13:49,443,422–49,445,325 | 131 bp | At TSS Multiome | 929 | |
| chr13:49,495,326–49,496,757 | 51.9 kb | Distal (>10kb) Multiome | 729 | |
| chr13:49,559,958–49,561,357 | 116.6 kb | Distal (>10kb) Multiome | 297 | |
| chr13:49,584,820–49,586,364 | 141.4 kb | Distal (>10kb) Multiome | 809 | |
| chr13:49,628,213–49,628,711 | 184.1 kb | Distal (>10kb) Multiome | 271 | |
| chr13:49,635,533–49,636,248 | 191.5 kb | Distal (>10kb) Multiome | 74 | |
| chr13:49,664,328–49,664,981 | 220.5 kb | Distal (>10kb) Multiome | 75 | |
| chr13:49,690,816–49,691,882 | 247.2 kb | Distal (>10kb) Multiome | 847 |
Genomic view of the SETDB2 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.