This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PHF2. 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 = PHF2 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 PHF2, 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 |
|---|---|---|---|---|
| chr9:93,133,298–93,134,791 | 442.5 kb | Distal (>10kb) Multiome HiCAR | 796 | |
| chr9:93,346,091–93,346,711 | 230.5 kb | Distal (>10kb) Multiome | 137 | |
| chr9:93,364,969–93,366,461 | 211.0 kb | Distal (>10kb) Multiome | 123 | |
| chr9:93,450,848–93,452,597 | 125.1 kb | Distal (>10kb) Multiome | 770 | |
| chr9:93,453,260–93,453,968 | 123.1 kb | Distal (>10kb) Multiome | 535 | |
| chr9:93,566,407–93,567,185 | 10.1 kb | Distal (>10kb) Multiome | 816 | |
| chr9:93,576,307–93,576,634 | 111 bp | At TSS | 250 | |
| chr9:93,576,737–93,577,071 | at TSS | At TSS | 160 | |
| chr9:93,826,327–93,826,940 | 249.7 kb | Distal (>10kb) Multiome | 168 | |
| chr9:93,827,082–93,828,691 | 251.0 kb | Distal (>10kb) Multiome | 373 |
Genomic view of the PHF2 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.