Expressive

rs1056522 (CHST13): Multi-tissue expression variant

Key takeaways

  • The ALT allele at rs1056522 consistently reduces CHST13 (C3orf22) gene expression across at least eight distinct tissue types.
  • The strongest expression-reducing effect appears in tibial nerve tissue.
  • Effects are consistent in direction across nerve, fat, spleen, blood, lung, artery, and skin.
  • This eQTL evidence comes from GTEx v11, a dataset of 953 individuals with strict false-discovery-rate control.
  • No disease or phenotype associations for this variant are documented in the provided studies.

Key takeaways

  • The ALT allele at rs1056522 consistently reduces CHST13 (C3orf22) gene expression across at least eight distinct tissue types.
  • The strongest expression-reducing effect appears in tibial nerve tissue.
  • Effects are consistent in direction across nerve, fat, spleen, blood, lung, artery, and skin.
  • This eQTL evidence comes from GTEx v11, a dataset of 953 individuals with strict false-discovery-rate control.
  • No disease or phenotype associations for this variant are documented in the provided studies.

What the research says rs1056522 is an expression quantitative trait locus (eQTL) - a genetic variant that influences how strongly a gene is expressed in cells - for CHST13, with the ALT allele associated with reduced expression across eight tissue types in GTEx v11 data from 953 donors, all meeting a false discovery rate (FDR) threshold below 5% GTEx Portal. Expression slopes range from -0.47 in sun-exposed lower-leg skin to -0.67 in tibial nerve (log2-normalized units), and the direction of effect is consistent across tissues as biologically distinct as visceral adipose, whole blood, and lung GTEx Portal.

Reported associations

  • CHST13 expression, tibial nerve: ALT allele associated with reduced expression (slope -0.67, p=7.0e-49) GTEx Portal
  • CHST13 expression, visceral adipose (omentum): ALT allele associated with reduced expression (slope -0.57, p=7.1e-38) GTEx Portal
  • CHST13 expression, spleen: ALT allele associated with reduced expression (slope -0.56, p=3.8e-26) GTEx Portal
  • CHST13 expression, subcutaneous adipose: ALT allele associated with reduced expression (slope -0.51, p=5.3e-37) GTEx Portal
  • CHST13 expression, whole blood: ALT allele associated with reduced expression (slope -0.51, p=4.1e-64) GTEx Portal
  • CHST13 expression, lung: ALT allele associated with reduced expression (slope -0.50, p=1.2e-39) GTEx Portal
  • CHST13 expression, tibial artery: ALT allele associated with reduced expression (slope -0.48, p=3.3e-33) GTEx Portal
  • CHST13 expression, sun-exposed skin (lower leg): ALT allele associated with reduced expression (slope -0.47, p=5.9e-28) GTEx Portal

Evidence quality All associations reported here derive from GTEx v11 cis-eQTL analysis (953 donors, FDR < 0.05), a well-validated reference resource for linking genetic variants to gene expression changes GTEx Portal. The replication of the expression-reducing effect across eight biologically distinct tissues strengthens confidence in the association. However, the four provided studies - covering scalable GWAS methodology for large biobank cohorts, mass spectrometry proteomics, protein ratio quantitative trait loci, and proteo-genomic disease mapping - do not report phenotypic or disease associations specific to this variant. Consequently, disease-level evidence is absent from the provided sources, and this entry should be considered preliminary in terms of trait-level associations.

Tissue-specific expression effects

  • CHST13: Reduced expression in tibial nerve (strongest effect among tissues reported), visceral adipose, spleen, subcutaneous adipose, whole blood, lung, tibial artery, and sun-exposed skin - all consistent in direction, with the ALT allele decreasing expression in every tissue tested GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What does rs1056522 do?

rs1056522 is an eQTL - a genetic variant that affects how much CHST13 gene product is made in cells. Carrying the ALT allele is associated with reduced CHST13 expression across at least eight tissue types.

What gene is rs1056522 linked to?

rs1056522 is an eQTL for CHST13, also designated C3orf22 for its location on chromosome 3. The variant affects how strongly this gene is expressed across a range of tissues.

Which tissues are affected by rs1056522?

GTEx v11 data identifies reduced CHST13 expression in tibial nerve, visceral adipose (omentum), spleen, subcutaneous adipose, whole blood, lung, tibial artery, and sun-exposed skin - all at FDR below 5%.

Is rs1056522 linked to any diseases?

The provided studies do not report disease or phenotype associations for rs1056522. The available evidence is limited to its consistent effect on CHST13 gene expression levels across multiple tissues.

How reliable is the evidence for rs1056522?

The eQTL associations come from GTEx v11 with 953 donors and FDR below 5%, a well-established large-scale reference dataset. The consistency of the effect across eight diverse tissues adds confidence, though disease-level evidence is not yet available in the provided sources.