This gene encodes a protein which was initially identified as a sphingomyelinase based on sequence similarity between bacterial sphingomyelinases and a yeast protein. Subsequent studies showed that its biological function is less likely to be as a sphingomyelinase and instead as a lysophospholipase. [provided by RefSeq, Oct 2009]
Transcription factors with Perturb-seq knockdown data for SMPD2. 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 = SMPD2 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 SMPD2, 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 |
|---|---|---|---|---|
| chr6:109,186,108–109,187,056 | 254.3 kb | Distal (>10kb) Multiome HiCAR | 39 | |
| chr6:109,236,275–109,236,762 | 204.1 kb | Distal (>10kb) Multiome | 258 | |
| chr6:109,381,700–109,383,452 | 58.0 kb | Distal (>10kb) Multiome | 1036 | |
| chr6:109,440,119–109,441,745 | 5 bp | At TSS Multiome | 863 | |
| chr6:109,454,912–109,456,586 | 15.2 kb | Distal (>10kb) Multiome HiCAR | 733 | |
| chr6:109,482,359–109,484,058 | 42.7 kb | Distal (>10kb) Multiome | 675 | |
| chr6:109,678,985–109,679,628 | 238.5 kb | Distal (>10kb) Multiome | 55 | |
| chr6:109,690,198–109,691,786 | 250.5 kb | Distal (>10kb) Multiome | 761 |
Genomic view of the SMPD2 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.