This gene is a member of the aggrecan/versican proteoglycan family. The protein encoded is a large chondroitin sulfate proteoglycan and is a major component of the extracellular matrix. This protein is involved in cell adhesion, proliferation, proliferation, migration and angiogenesis and plays a central role in tissue morphogenesis and maintenance. Mutations in this gene are the cause of Wagner syndrome type 1. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]
Transcription factors with Perturb-seq knockdown data for VCAN. 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 = VCAN 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 VCAN, 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 |
|---|---|---|---|---|
| chr5:82,277,759–82,278,896 | 1193.1 kb | Distal (>10kb) Multiome HiCAR | 836 | |
| chr5:82,293,939–82,294,938 | 1177.2 kb | Distal (>10kb) Multiome HiCAR | 132 | |
| chr5:83,076,893–83,078,174 | 394.1 kb | Distal (>10kb) Multiome HiCAR | 808 | |
| chr5:83,177,626–83,178,521 | 293.7 kb | Distal (>10kb) Multiome HiCAR | 101 | |
| chr5:83,354,732–83,355,974 | 116.4 kb | Distal (>10kb) Multiome | 327 | |
| chr5:83,465,707–83,466,172 | 5.4 kb | Proximal (<10kb) | 63 | |
| chr5:83,470,946–83,472,020 | 183 bp | At TSS Multiome | 379 | |
| chr5:83,472,395–83,475,303 | 3.0 kb | Proximal (<10kb) Multiome | 827 | |
| chr5:83,475,950–83,476,273 | 4.3 kb | Proximal (<10kb) | 144 | |
| chr5:83,493,487–83,495,007 | 23.0 kb | Distal (>10kb) Multiome | 320 | |
| chr5:83,714,660–83,715,756 | 243.4 kb | Distal (>10kb) Multiome | 275 | |
| chr5:83,720,773–83,722,967 | 250.8 kb | Distal (>10kb) Multiome | 698 |
Genomic view of the VCAN 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.