The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a cause of Schimke immunoosseous dysplasia (SIOD), an autosomal recessive disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction, and T-cell immunodeficiency. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for SMARCAL1. 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 = SMARCAL1 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 SMARCAL1, 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 |
|---|---|---|---|---|
| chr2:216,114,288–216,115,514 | 297.6 kb | Distal (>10kb) Multiome | 671 | |
| chr2:216,275,236–216,275,858 | 137.0 kb | Distal (>10kb) Multiome | 120 | |
| chr2:216,283,571–216,284,041 | 128.7 kb | Distal (>10kb) Multiome | 206 | |
| chr2:216,292,640–216,293,553 | 119.3 kb | Distal (>10kb) Multiome | 205 | |
| chr2:216,317,598–216,318,777 | 94.6 kb | Distal (>10kb) Multiome | 193 | |
| chr2:216,339,679–216,340,452 | 72.3 kb | Distal (>10kb) Multiome | 192 | |
| chr2:216,345,559–216,346,320 | 66.5 kb | Distal (>10kb) Multiome | 100 | |
| chr2:216,370,964–216,372,465 | 40.2 kb | Distal (>10kb) Multiome | 850 | |
| chr2:216,404,114–216,404,245 | 8.2 kb | Proximal (<10kb) | 66 | |
| chr2:216,412,020–216,413,196 | 39 bp | At TSS Multiome | 882 | |
| chr2:216,498,326–216,499,289 | 86.4 kb | Distal (>10kb) Multiome | 982 | |
| chr2:216,606,380–216,607,387 | 194.3 kb | Distal (>10kb) Multiome | 243 | |
| chr2:216,619,507–216,620,419 | 207.5 kb | Distal (>10kb) Multiome | 382 | |
| chr2:216,632,597–216,634,235 | 220.9 kb | Distal (>10kb) Multiome | 459 | |
| chr2:216,635,691–216,637,041 | 224.3 kb | Distal (>10kb) Multiome | 263 | |
| chr2:216,665,266–216,666,969 | 253.2 kb | Distal (>10kb) Multiome | 454 | |
| chr2:216,691,972–216,693,060 | 279.8 kb | Distal (>10kb) Multiome | 383 | |
| chr2:216,694,105–216,695,084 | 282.0 kb | Distal (>10kb) Multiome | 316 | |
| chr2:216,695,439–216,696,027 | 283.3 kb | Distal (>10kb) Multiome | 258 | |
| chr2:216,765,712–216,766,366 | 353.6 kb | Distal (>10kb) Multiome | 240 |
Genomic view of the SMARCAL1 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.