Expressive

rs115354241 (LINC01258): Brain Expression Variant

Key takeaways

  • rs115354241 sits in LINC01258, a non-coding RNA gene with expression detected in brain tissue
  • The ALT allele is linked to increased LINC01258 expression in the brain's substantia nigra
  • This variant appears in the context of one of the largest all-cause and vascular dementia genetics studies conducted to date
  • The gene expression link is mechanistic and does not on its own predict health outcomes
  • Direct evidence connecting rs115354241 to specific disease risk is limited in available study materials

Key takeaways

  • rs115354241 is located in LINC01258, a long intergenic non-coding RNA gene with expression detected in brain tissue
  • The ALT allele is linked to increased LINC01258 expression in the brain's substantia nigra, based on GTEx eQTL data
  • A large genome-wide association meta-analysis of all-cause dementia and vascular dementia (over 800,000 individuals) provides the disease-domain context for this locus
  • The eQTL link is mechanistic, establishing a relationship between the variant and gene expression levels, not a direct health outcome
  • Direct evidence connecting rs115354241 to specific disease risk is limited in the available study materials

What the research says LINC01258 (a long intergenic non-coding RNA, meaning it produces RNA molecules rather than proteins) is expressed in brain tissue. A genome-wide association meta-analysis of all-cause dementia (ACD) and vascular dementia (VaD) used data from 800,597 individuals including 46,902 ACD cases and 8,702 VaD cases, published in Alzheimer's & Dementia (2024); this study provides disease-domain context for the locus, though the provided text does not name rs115354241 among its explicitly reported novel findings. GTEx v11 eQTL data (953 donors) show that the ALT allele of rs115354241 is associated with increased expression of this gene in the brain's substantia nigra (slope +1.24 log2-normalized units, p=1.1e-5) GTEx Portal.

Reported associations

  • All-cause and vascular dementia (contextual): A large GWAS meta-analysis investigated genetic risk for ACD and VaD, identifying novel loci linked to neurodegeneration, vascular risk factors, and cerebral small vessel disease; rs115354241 is associated with the LINC01258 locus within this disease domain, though the provided study excerpt does not list this variant as a named finding.
  • Brain substantia nigra gene expression: The ALT allele is associated with increased LINC01258 expression in this brain tissue GTEx Portal.

Evidence quality The dementia GWAS that provides disease-domain context is among the largest of its kind (n=800,597, including 46,902 ACD cases and 8,702 VaD cases), lending substantial statistical power to its overall findings. However, because the provided study excerpt does not report rs115354241 as an explicitly named associated locus, its specific p-value, effect size, and replication status within that study cannot be confirmed from available materials. The GTEx eQTL finding (p=1.1e-5, n=953 donors) reaches nominal significance and establishes a link between the ALT allele and increased LINC01258 expression in the brain's substantia nigra GTEx Portal; eQTL data demonstrate mechanism, not causality for any health outcome. Overall, the evidence for this variant is preliminary and limited to a mechanistic expression link.

Tissue-specific expression effects

  • LINC01258: The ALT allele is associated with increased expression in brain substantia nigra tissue GTEx Portal.

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is LINC01258?

LINC01258 is a long intergenic non-coding RNA, meaning it is a gene that produces RNA molecules but does not code for a protein. It has detectable expression in brain tissue according to GTEx reference data.

What does rs115354241 do?

The ALT allele of rs115354241 is associated with increased LINC01258 expression in the brain's substantia nigra, based on GTEx eQTL (expression quantitative trait locus) data. This is a mechanistic finding about gene activity levels, not a direct health or disease prediction.

Is rs115354241 linked to dementia?

This variant is associated with the LINC01258 locus, which appears in the context of a large genome-wide association study of all-cause dementia and vascular dementia involving over 800,000 individuals. However, the available study text does not confirm it as an explicitly named associated variant, so any link to dementia risk should be considered preliminary.

What is an eQTL, and why does it matter?

An eQTL (expression quantitative trait locus) is a genetic variant associated with differences in how much a gene is expressed in a tissue. An eQTL finding shows a mechanistic link between a variant and gene activity levels, but does not by itself establish a cause-and-effect relationship with a health outcome.

How confident are researchers about this variant's effects?

The evidence is preliminary. The GTEx eQTL data shows a nominally significant association (p=1.1e-5) with increased brain expression in the substantia nigra, but the provided dementia study text does not explicitly name rs115354241 as a confirmed associated locus, leaving its disease relevance uncertain.