This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for COL9A1. 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 = COL9A1 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 COL9A1, 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 |
|---|---|---|---|---|
| chr6:70,280,303–70,280,910 | 2.3 kb | Proximal (<10kb) | 121 | |
| chr6:70,281,923–70,283,789 | 149 bp | At TSS Multiome | 386 | |
| chr6:70,289,404–70,289,557 | 6.2 kb | Proximal (<10kb) | 16 | |
| chr6:70,291,138–70,291,589 | 7.9 kb | Proximal (<10kb) | 76 | |
| chr6:70,291,768–70,292,539 | 8.6 kb | Proximal (<10kb) | 61 | |
| chr6:70,412,616–70,414,468 | 130.2 kb | Distal (>10kb) Multiome | 868 | |
| chr6:70,566,096–70,567,415 | 283.7 kb | Distal (>10kb) Multiome | 830 |
Genomic view of the COL9A1 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.