This gene is located in a cluster of imprinted genes on chromosome 11p15.5, which is considered to be an important tumor suppressor gene region. Alterations in this region may be associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. This gene has been shown to be imprinted, with preferential expression from the maternal allele in placenta and liver. [provided by RefSeq, Oct 2010]
Transcription factors with Perturb-seq knockdown data for PHLDA2. 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 = PHLDA2 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 PHLDA2, 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 |
|---|---|---|---|---|
| chr11:2,420,598–2,421,164 | 508.6 kb | Distal (>10kb) Multiome HiCAR | 385 | |
| chr11:2,532,598–2,533,458 | 396.5 kb | Distal (>10kb) Multiome HiCAR | 567 | |
| chr11:2,693,272–2,694,189 | 235.8 kb | Distal (>10kb) Multiome | 236 | |
| chr11:2,699,491–2,700,586 | 229.3 kb | Distal (>10kb) Multiome | 879 | |
| chr11:2,862,328–2,863,500 | 66.9 kb | Distal (>10kb) Multiome | 132 | |
| chr11:2,883,795–2,886,948 | 43.4 kb | Distal (>10kb) Multiome | 639 | |
| chr11:2,891,828–2,893,111 | 36.9 kb | Distal (>10kb) Multiome | 572 | |
| chr11:2,901,621–2,903,073 | 27.2 kb | Distal (>10kb) Multiome | 610 | |
| chr11:2,928,807–2,931,249 | 1.5 kb | Proximal (<10kb) Multiome | 770 | |
| chr11:2,933,509–2,934,319 | 4.1 kb | Proximal (<10kb) | 195 | |
| chr11:2,991,519–2,993,201 | 63.0 kb | Distal (>10kb) Multiome | 759 | |
| chr11:3,056,953–3,057,972 | 128.1 kb | Distal (>10kb) Multiome | 798 | |
| chr11:3,091,645–3,092,317 | 162.5 kb | Distal (>10kb) Multiome | 449 | |
| chr11:3,160,043–3,161,026 | 231.1 kb | Distal (>10kb) Multiome | 283 |
Genomic view of the PHLDA2 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.