Expressive

rs118102940 (GNPTAB): CHPT1 Expression QTL

Key takeaways

  • rs118102940, in the GNPTAB gene region, influences expression of the nearby CHPT1 gene in multiple tissue types.
  • The alternative allele is linked to increased CHPT1 expression in fibroblasts, heart tissue, fat, and skin, based on GTEx data from 953 donors.
  • No disease or complex trait associations for this variant appear in the provided research literature.
  • Evidence is limited to gene expression effects and should be treated as preliminary.

Key takeaways

  • rs118102940, in the GNPTAB gene region, influences expression of the nearby CHPT1 gene in multiple tissue types.
  • The alternative allele is linked to increased CHPT1 expression in fibroblasts, heart tissue, fat, and skin, based on GTEx data from 953 donors.
  • No disease or complex trait associations for this variant appear in the provided research literature.
  • Evidence is limited to gene expression effects and should be treated as preliminary.

What the research says rs118102940 is annotated to the GNPTAB gene and functions as a cis-eQTL (a genetic variant that influences the expression of a physically nearby gene, detected within a defined genomic window) for CHPT1, with associations found across four tissue types at FDR < 0.05 in GTEx v11 data from 953 donors GTEx Portal. The alternative allele is consistently associated with higher CHPT1 expression, with effect size slopes ranging from +0.26 in sun-exposed lower leg skin to +0.45 in cultured fibroblasts GTEx Portal. No specific disease or trait association for this variant was documented in the provided GWAS literature.

Reported associations

  • CHPT1 expression in cultured fibroblasts: Alternative allele associated with increased expression; slope +0.45, p = 5.1e-5 GTEx Portal
  • CHPT1 expression in heart atrial appendage: Alternative allele associated with increased expression; slope +0.36, p = 1.1e-5 GTEx Portal
  • CHPT1 expression in subcutaneous adipose tissue: Alternative allele associated with increased expression; slope +0.32, p = 1.0e-5 GTEx Portal
  • CHPT1 expression in sun-exposed lower leg skin: Alternative allele associated with increased expression; slope +0.26, p = 2.3e-4 GTEx Portal

Evidence quality All available evidence for rs118102940 comes from the GTEx v11 eQTL analysis (953 donors), which detected consistent positive associations between the alternative allele and CHPT1 expression across four tissues, all passing FDR < 0.05, with p-values ranging from 1.0e-5 to 2.3e-4 GTEx Portal. The consistent direction of effect across tissue types lends some confidence to the eQTL finding. However, no independent replication in a separate cohort is documented in the provided materials, no trait-level or disease GWAS associations were reported for this variant, and the evidence base is restricted entirely to gene expression data. The current evidence for this variant should be treated as preliminary.

Tissue-specific expression effects

  • CHPT1: Increased expression in cultured fibroblasts, heart atrial appendage, subcutaneous adipose tissue, and sun-exposed lower leg skin, with the alternative allele consistently linked to higher expression across all four tissues GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs118102940?

rs118102940 is a single nucleotide polymorphism, meaning a position in the genome where one DNA letter varies between individuals, annotated to the GNPTAB gene region. Based on current data, it is primarily characterized as a genetic regulator of nearby CHPT1 gene expression.

What effect does rs118102940 have on CHPT1 expression?

The alternative allele at rs118102940 is associated with higher CHPT1 expression in four tissue types: cultured fibroblasts, heart atrial appendage, subcutaneous fat, and sun-exposed lower leg skin. The association is consistent in direction across all four tissues in GTEx v11 data from 953 donors.

Is rs118102940 linked to any disease?

No disease or complex trait associations for rs118102940 were documented in the studies provided. The available evidence is limited to gene expression effects in the GTEx dataset, and findings should be treated as preliminary.

Why does rs118102940 affect CHPT1 if it is located in the GNPTAB gene?

The GTEx eQTL analysis searches for expression effects within a cis-window, meaning a defined genomic neighborhood around each variant. rs118102940 is annotated to GNPTAB by position, but the analysis detected its strongest expression associations with the neighboring CHPT1 gene rather than GNPTAB itself.