The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which 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 and contains a predicted leucine zipper motif typical of many transcription factors. [provided by RefSeq, Jul 2008]
Modules significantly affected by knockdown. ↑ Up = module upregulated upon KD; ↓ Down = module downregulated upon KD.
| Cluster | Dir | NES | padj | Bind | OR | padj (bind) |
|---|
| Module | Dir | NES | #gRNA | padj | Bind | OR | padj (bind) |
|---|
| Submodule | Module | Dir | NES | #gRNA | Bind | OR | padj (bind) |
|---|
Genes likely regulated by SMARCC1 through linked binding evidence in open chromatin. The chart ranks TF-linked genes by their mean Perturb-seq response to SMARCC1 knockdown, with negative coefficients indicating downregulation and positive coefficients indicating upregulation upon knockdown.
Open chromatin elements (ATAC-seq) where SMARCC1 has ChIP-seq or motif footprint binding evidence and which are linked to at least one target gene region.
| Element | Size | Linked genes |
|---|
Transcription factors with Perturb-seq knockdown data for SMARCC1. 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 = SMARCC1 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 SMARCC1, 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 |
|---|---|---|---|---|
| chr3:47,512,910–47,514,044 | 268.3 kb | Distal (>10kb) Multiome | 892 | |
| chr3:47,522,175–47,522,702 | 259.5 kb | Distal (>10kb) Multiome HiCAR | 591 | |
| chr3:47,577,493–47,579,738 | 202.5 kb | Distal (>10kb) Multiome | 446 | |
| chr3:47,781,220–47,782,492 | 42 bp | At TSS Multiome | 965 | |
| chr3:47,789,088–47,789,393 | 7.2 kb | Proximal (<10kb) | 471 | |
| chr3:47,802,571–47,803,701 | 21.3 kb | Distal (>10kb) Multiome | 820 | |
| chr3:47,824,603–47,825,589 | 43.1 kb | Distal (>10kb) Multiome | 882 |
Genomic view of the SMARCC1 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.