The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues. Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element. Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the autosomal dominant disorder, Bethlem myopathy. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for COL6A1. 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 = COL6A1 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 COL6A1, 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 |
|---|---|---|---|---|
| chr21:45,970,520–45,971,289 | 11.0 kb | Distal (>10kb) Multiome | 325 | |
| chr21:45,972,497–45,973,054 | 8.7 kb | Proximal (<10kb) | 201 | |
| chr21:45,973,174–45,975,630 | 7.8 kb | Proximal (<10kb) Multiome | 597 | |
| chr21:45,975,731–45,976,305 | 5.5 kb | Proximal (<10kb) | 48 | |
| chr21:45,977,133–45,977,741 | 4.0 kb | Proximal (<10kb) | 72 | |
| chr21:45,981,076–45,982,605 | 178 bp | At TSS Multiome | 580 | |
| chr21:46,097,574–46,098,972 | 116.3 kb | Distal (>10kb) Multiome HiCAR | 294 | |
| chr21:46,153,138–46,153,696 | 171.7 kb | Distal (>10kb) Multiome | 515 | |
| chr21:46,184,645–46,185,202 | 202.9 kb | Distal (>10kb) Multiome | 334 | |
| chr21:46,228,249–46,230,022 | 247.2 kb | Distal (>10kb) Multiome | 833 |
Genomic view of the COL6A1 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.