This gene encodes a Polycomb group protein. The protein is a component of a histone H3 lysine-27 (H3K27)-specific methyltransferase complex, and functions in transcriptional repression of homeotic genes. The protein is also recruited to double-strand breaks, and reduced protein levels results in X-ray sensitivity and increased homologous recombination. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
Transcription factors with Perturb-seq knockdown data for PHF1. 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 = PHF1 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 PHF1, 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 |
|---|---|---|---|---|
| chr6:33,161,505–33,162,100 | 248.7 kb | Distal (>10kb) Multiome | 589 | |
| chr6:33,199,801–33,201,289 | 209.7 kb | Distal (>10kb) Multiome | 1049 | |
| chr6:33,204,263–33,205,422 | 205.8 kb | Distal (>10kb) Multiome | 762 | |
| chr6:33,208,069–33,208,990 | 201.8 kb | Distal (>10kb) Multiome | 858 | |
| chr6:33,248,132–33,249,983 | 162.1 kb | Distal (>10kb) Multiome | 961 | |
| chr6:33,271,370–33,272,508 | 138.4 kb | Distal (>10kb) Multiome | 1058 | |
| chr6:33,276,685–33,277,905 | 133.0 kb | Distal (>10kb) Multiome | 807 | |
| chr6:33,288,941–33,289,881 | 121.0 kb | Distal (>10kb) Multiome | 701 | |
| chr6:33,297,445–33,300,232 | 112.5 kb | Distal (>10kb) Multiome | 1095 | |
| chr6:33,312,436–33,314,207 | 97.5 kb | Distal (>10kb) Multiome | 795 | |
| chr6:33,317,189–33,318,504 | 92.5 kb | Distal (>10kb) Multiome | 649 | |
| chr6:33,322,636–33,323,832 | 87.3 kb | Distal (>10kb) Multiome | 941 | |
| chr6:33,346,609–33,347,126 | 63.6 kb | Distal (>10kb) Multiome | 37 | |
| chr6:33,390,888–33,392,247 | 18.8 kb | Distal (>10kb) Multiome | 993 | |
| chr6:33,409,936–33,411,502 | 97 bp | At TSS Multiome | 977 | |
| chr6:33,417,606–33,419,249 | 7.9 kb | Proximal (<10kb) Multiome | 973 | |
| chr6:33,419,793–33,420,532 | 9.8 kb | Proximal (<10kb) Multiome | 162 | |
| chr6:33,425,590–33,426,362 | 15.5 kb | Distal (>10kb) Multiome | 665 | |
| chr6:33,431,024–33,432,096 | 20.8 kb | Distal (>10kb) Multiome | 337 | |
| chr6:33,454,074–33,454,852 | 44.1 kb | Distal (>10kb) Multiome | 906 | |
| chr6:33,547,185–33,548,324 | 137.3 kb | Distal (>10kb) Multiome | 155 | |
| chr6:33,570,899–33,571,638 | 161.0 kb | Distal (>10kb) Multiome | 755 | |
| chr6:33,579,935–33,580,700 | 169.9 kb | Distal (>10kb) Multiome | 639 | |
| chr6:33,592,764–33,593,449 | 182.6 kb | Distal (>10kb) Multiome | 224 | |
| chr6:33,620,828–33,622,474 | 211.6 kb | Distal (>10kb) Multiome | 594 | |
| chr6:33,632,607–33,634,721 | 222.3 kb | Distal (>10kb) Multiome | 600 |
Genomic view of the PHF1 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.