Expressive

rs115504008 (COL9A2): Tissue Expression Variant

Key takeaways

  • The ALT allele at rs115504008 is linked to lower COL9A2 expression in subcutaneous fat, tibial nerve, stomach, and EBV-transformed immune cells
  • The same allele also reduces a separate gene, OXCT2, specifically in the brain amygdala
  • These are expression-level findings based on GTEx v11 data from 953 donors, not confirmed disease associations
  • The OXCT2 effect in the amygdala (slope -0.46) is larger than the COL9A2 effects across tissues (slopes -0.14 to -0.23)

Key takeaways

  • The ALT allele at rs115504008 is associated with lower COL9A2 expression in subcutaneous fat, tibial nerve, stomach, and EBV-transformed immune cells
  • The same allele also reduces expression of a separate gene, OXCT2, in the brain amygdala
  • These are expression-level (eQTL) findings; no confirmed disease or phenotype associations are described in the available sources
  • The effect on OXCT2 in the brain amygdala (log2 slope -0.46) is notably larger than the COL9A2 effects across tissues (slopes -0.14 to -0.23)

What the research says GTEx v11 eQTL analysis (953 donors, cis-window, FDR<0.05) shows that the ALT allele at rs115504008 is associated with reduced COL9A2 expression across four tissues: subcutaneous adipose, tibial nerve, stomach, and EBV-transformed lymphocytes GTEx Portal. The same allele is also associated with reduced expression of OXCT2, a separate gene, specifically in the brain amygdala GTEx Portal. The available sources provide expression-level associations only; no confirmed disease or trait associations for this specific variant are documented in the provided study data.

Reported associations

  • COL9A2 expression (EBV-transformed lymphocytes): ALT allele associated with reduced expression (slope -0.23, p=1.7e-7) GTEx Portal
  • COL9A2 expression (subcutaneous adipose): ALT allele associated with reduced expression (slope -0.20, p=1.2e-8) GTEx Portal
  • COL9A2 expression (tibial nerve): ALT allele associated with reduced expression (slope -0.14, p=5.5e-6) GTEx Portal
  • COL9A2 expression (stomach): ALT allele associated with reduced expression (slope -0.14, p=7.4e-6) GTEx Portal
  • OXCT2 expression (brain amygdala): ALT allele associated with reduced expression (slope -0.46, p=4.7e-6) GTEx Portal

Evidence quality All reported associations for rs115504008 in the available sources are expression quantitative trait loci (eQTL) findings from GTEx v11, derived from 953 donors using a cis-window analysis at FDR<0.05 GTEx Portal. The log2-normalized effect sizes (slopes) for COL9A2 range from -0.14 to -0.23 across tissues, while the OXCT2 effect in the brain amygdala is -0.46, indicating a somewhat larger relative expression difference at that locus. These slopes reflect direction and relative magnitude of the variant's influence on gene activity, not disease risk or clinical outcome. No replicated phenotype-level associations are documented for this specific variant in the provided study data, so the clinical significance of these expression effects remains to be established and should be considered preliminary.

Tissue-specific expression effects

  • COL9A2: The ALT allele is associated with reduced expression in EBV-transformed lymphocytes, subcutaneous adipose tissue, tibial nerve, and stomach GTEx Portal
  • OXCT2: The ALT allele is associated with reduced expression in the brain amygdala GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs115504008?

rs115504008 is a genetic variant in the COL9A2 gene region. Carrying the ALT allele is associated with reduced activity of the COL9A2 gene in several tissues and reduced activity of a second gene, OXCT2, in the brain amygdala.

Which tissues are affected by rs115504008?

GTEx v11 data shows that the ALT allele reduces COL9A2 expression in subcutaneous fat, tibial nerve, stomach, and EBV-transformed lymphocytes (an immune cell type). The same allele also reduces OXCT2 expression in the brain amygdala.

Is rs115504008 linked to any disease?

The available evidence covers gene expression effects only. No confirmed disease or phenotype associations for rs115504008 are described in the sources reviewed. The findings are considered preliminary.

How strong is the evidence for rs115504008?

Associations are based on GTEx v11 eQTL data from 953 donors, all meeting FDR<0.05. Effect sizes are modest to moderate (log2 slopes from -0.14 to -0.46). These are expression-level associations, and their link to any health outcome has not been established in the available data.

What is an eQTL and why does it matter for this variant?

An eQTL (expression quantitative trait locus) is a genetic variant statistically associated with changes in how active a gene is in specific tissues. For rs115504008, the ALT allele is linked to lower activity of COL9A2 and OXCT2 in the tissues described, which may inform future research into the biological role of this variant, but does not by itself predict any disease or condition.