The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. N-terminal part of this PTP contains two tandem Src homolog (SH2) domains, which act as protein phospho-tyrosine binding domains, and mediate the interaction of this PTP with its substrates. This PTP is expressed primarily in hematopoietic cells, and functions as an important regulator of multiple signaling pathways in hematopoietic cells. This PTP has been shown to interact with, and dephosphorylate a wide spectrum of phospho-proteins involved in hematopoietic cell signaling. Multiple alternatively spliced variants of this gene, which encode distinct isoforms, have been reported. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PTPN6. 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 = PTPN6 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 PTPN6, 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 |
|---|---|---|---|---|
| chr12:6,662,802–6,663,663 | 283.2 kb | Distal (>10kb) Multiome | 868 | |
| chr12:6,688,517–6,690,027 | 257.0 kb | Distal (>10kb) Multiome | 943 | |
| chr12:6,699,959–6,700,887 | 246.0 kb | Distal (>10kb) Multiome | 263 | |
| chr12:6,723,658–6,724,773 | 222.4 kb | Distal (>10kb) Multiome | 1065 | |
| chr12:6,752,554–6,754,332 | 193.0 kb | Distal (>10kb) Multiome | 975 | |
| chr12:6,763,677–6,764,983 | 182.1 kb | Distal (>10kb) Multiome | 570 | |
| chr12:6,765,172–6,767,791 | 180.1 kb | Distal (>10kb) Multiome | 824 | |
| chr12:6,768,329–6,769,331 | 177.4 kb | Distal (>10kb) Multiome | 249 | |
| chr12:6,778,736–6,779,459 | 167.4 kb | Distal (>10kb) Multiome | 777 | |
| chr12:6,821,268–6,822,155 | 124.7 kb | Distal (>10kb) Multiome | 299 | |
| chr12:6,825,458–6,825,915 | 120.8 kb | Distal (>10kb) Multiome | 404 | |
| chr12:6,828,101–6,829,966 | 116.9 kb | Distal (>10kb) Multiome | 689 | |
| chr12:6,851,017–6,853,279 | 94.1 kb | Distal (>10kb) Multiome | 966 | |
| chr12:6,866,801–6,870,175 | 79.0 kb | Distal (>10kb) Multiome | 887 | |
| chr12:6,871,062–6,874,199 | 74.1 kb | Distal (>10kb) Multiome HiCAR | 947 | |
| chr12:6,890,735–6,891,820 | 55.3 kb | Distal (>10kb) Multiome | 908 | |
| chr12:6,904,217–6,905,282 | 41.6 kb | Distal (>10kb) Multiome | 566 | |
| chr12:6,914,274–6,914,898 | 32.0 kb | Distal (>10kb) Multiome | 536 | |
| chr12:6,924,156–6,924,592 | 22.0 kb | Distal (>10kb) Multiome | 458 | |
| chr12:6,925,828–6,926,431 | 20.5 kb | Distal (>10kb) Multiome HiCAR | 407 | |
| chr12:6,927,411–6,928,051 | 18.6 kb | Distal (>10kb) Multiome HiCAR | 493 | |
| chr12:6,936,709–6,938,342 | 8.4 kb | Proximal (<10kb) Multiome HiCAR | 1008 | |
| chr12:6,942,356–6,945,492 | 2.3 kb | Proximal (<10kb) Multiome | 1205 | |
| chr12:6,945,587–6,947,099 | 14 bp | At TSS Multiome | 618 | |
| chr12:6,961,769–6,963,542 | 16.7 kb | Distal (>10kb) Multiome | 682 | |
| chr12:6,964,932–6,965,569 | 18.8 kb | Distal (>10kb) Multiome | 549 | |
| chr12:6,970,111–6,971,189 | 24.3 kb | Distal (>10kb) Multiome | 899 | |
| chr12:7,018,028–7,019,126 | 72.2 kb | Distal (>10kb) Multiome | 824 | |
| chr12:7,108,059–7,109,582 | 162.8 kb | Distal (>10kb) Multiome HiCAR | 818 | |
| chr12:7,129,788–7,131,412 | 183.8 kb | Distal (>10kb) Multiome | 619 | |
| chr12:7,188,394–7,190,508 | 242.1 kb | Distal (>10kb) Multiome | 769 | |
| chr12:8,026,338–8,027,323 | 1080.4 kb | Distal (>10kb) Multiome HiCAR | 935 |
Genomic view of the PTPN6 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.