The protein encoded by this gene is a member of the SWI/SNF family of proteins and is highly similar to the brahma protein of Drosophila. 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 is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a trinucleotide repeat (CAG) length polymorphism. [provided by RefSeq, Jan 2014]
Transcription factors with Perturb-seq knockdown data for SMARCA2. 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 = SMARCA2 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 SMARCA2, 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 |
|---|---|---|---|---|
| chr9:2,014,443–2,018,701 | 143.3 kb | Distal (>10kb) Multiome | 949 | |
| chr9:2,158,166–2,158,593 | at TSS | At TSS | 243 | |
| chr9:2,159,776–2,160,188 | 1.3 kb | Proximal (<10kb) | 72 | |
| chr9:2,161,748–2,162,012 | 3.3 kb | Proximal (<10kb) | 24 | |
| chr9:2,241,108–2,243,366 | 83.5 kb | Distal (>10kb) Multiome | 876 | |
| chr9:2,280,841–2,282,179 | 123.0 kb | Distal (>10kb) Multiome | 259 | |
| chr9:2,283,300–2,283,939 | 125.2 kb | Distal (>10kb) Multiome | 77 | |
| chr9:2,420,269–2,421,188 | 262.3 kb | Distal (>10kb) Multiome HiCAR | 122 | |
| chr9:2,620,982–2,623,801 | 463.1 kb | Distal (>10kb) Multiome HiCAR | 768 | |
| chr9:2,816,339–2,817,126 | 658.3 kb | Distal (>10kb) Multiome HiCAR | 152 | |
| chr9:2,843,166–2,844,741 | 685.7 kb | Distal (>10kb) Multiome HiCAR | 860 |
Genomic view of the SMARCA2 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.