The protein encoded by this gene is a lysosomal acid sphingomyelinase that converts sphingomyelin to ceramide. The encoded protein also has phospholipase C activity. Defects in this gene are a cause of Niemann-Pick disease type A (NPA) and Niemann-Pick disease type B (NPB). Multiple transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]
Transcription factors with Perturb-seq knockdown data for SMPD1. 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 = SMPD1 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 SMPD1, 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 |
|---|---|---|---|---|
| chr11:6,234,062–6,235,769 | 155.6 kb | Distal (>10kb) Multiome | 776 | |
| chr11:6,237,822–6,239,512 | 151.6 kb | Distal (>10kb) Multiome | 164 | |
| chr11:6,249,589–6,250,614 | 140.5 kb | Distal (>10kb) Multiome | 268 | |
| chr11:6,251,174–6,251,654 | 139.1 kb | Distal (>10kb) Multiome | 193 | |
| chr11:6,258,709–6,260,456 | 130.8 kb | Distal (>10kb) Multiome | 283 | |
| chr11:6,267,833–6,269,111 | 122.0 kb | Distal (>10kb) Multiome | 142 | |
| chr11:6,280,060–6,282,351 | 109.7 kb | Distal (>10kb) Multiome | 214 | |
| chr11:6,318,947–6,321,304 | 70.5 kb | Distal (>10kb) Multiome | 591 | |
| chr11:6,353,367–6,353,932 | 36.9 kb | Distal (>10kb) Multiome | 395 | |
| chr11:6,367,341–6,367,799 | 23.0 kb | Distal (>10kb) Multiome | 55 | |
| chr11:6,386,681–6,386,953 | 3.5 kb | Proximal (<10kb) | 3 | |
| chr11:6,389,605–6,390,990 | 129 bp | At TSS Multiome | 752 | |
| chr11:6,418,399–6,419,618 | 28.6 kb | Distal (>10kb) Multiome HiCAR | 494 | |
| chr11:6,468,896–6,469,642 | 78.8 kb | Distal (>10kb) Multiome | 253 | |
| chr11:6,473,129–6,474,612 | 83.6 kb | Distal (>10kb) Multiome | 591 | |
| chr11:6,480,885–6,482,114 | 90.9 kb | Distal (>10kb) Multiome | 828 | |
| chr11:6,603,192–6,604,726 | 213.3 kb | Distal (>10kb) Multiome | 908 | |
| chr11:6,606,600–6,607,433 | 216.6 kb | Distal (>10kb) Multiome | 532 | |
| chr11:6,611,505–6,613,097 | 221.9 kb | Distal (>10kb) Multiome | 996 | |
| chr11:6,618,753–6,619,738 | 229.0 kb | Distal (>10kb) Multiome | 587 | |
| chr11:6,629,672–6,631,067 | 240.0 kb | Distal (>10kb) Multiome | 226 | |
| chr11:6,655,068–6,656,298 | 265.3 kb | Distal (>10kb) Multiome | 314 | |
| chr11:6,682,693–6,683,793 | 293.0 kb | Distal (>10kb) Multiome | 950 |
Genomic view of the SMPD1 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.