Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in heterochromatin formation and negative regulation of DNA-templated transcription. Predicted to act upstream of or within anterior/posterior pattern specification; chromatin remodeling; and spermatogenesis. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
Modules significantly affected by knockdown. ↑ Up = module upregulated upon KD; ↓ Down = module downregulated upon KD.
| Module | Dir | NES | #gRNA | padj | Bind | OR | padj (bind) |
|---|
| Submodule | Module | Dir | NES | #gRNA | Bind | OR | padj (bind) |
|---|
Genes likely regulated by SCMH1 through linked binding evidence in open chromatin. The chart ranks TF-linked genes by their mean Perturb-seq response to SCMH1 knockdown, with negative coefficients indicating downregulation and positive coefficients indicating upregulation upon knockdown.
Open chromatin elements (ATAC-seq) where SCMH1 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 SCMH1. 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 = SCMH1 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 SCMH1, 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 |
|---|---|---|---|---|
| chr1:40,952,369–40,952,943 | 289.7 kb | Distal (>10kb) Multiome | 442 | |
| chr1:40,978,861–40,980,635 | 262.5 kb | Distal (>10kb) Multiome | 809 | |
| chr1:41,021,596–41,022,211 | 220.4 kb | Distal (>10kb) Multiome | 181 | |
| chr1:41,150,793–41,151,314 | 91.2 kb | Distal (>10kb) Multiome | 272 | |
| chr1:41,241,300–41,242,832 | 162 bp | At TSS Multiome | 773 | |
| chr1:41,341,206–41,342,779 | 99.9 kb | Distal (>10kb) Multiome | 385 | |
| chr1:41,360,298–41,362,650 | 118.9 kb | Distal (>10kb) Multiome | 692 | |
| chr1:41,432,518–41,433,186 | 190.6 kb | Distal (>10kb) Multiome | 530 | |
| chr1:41,496,061–41,496,989 | 254.1 kb | Distal (>10kb) Multiome | 581 | |
| chr1:41,515,924–41,516,803 | 274.0 kb | Distal (>10kb) Multiome | 500 |
Genomic view of the SCMH1 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.