rs116092581 (LINC02609): Esophageal Expression Variant

Q: What is the LINC02609 gene?

LINC02609 is a long intergenic non-coding RNA (lincRNA), a type of RNA molecule that does not produce protein but can influence the activity of nearby genes. Its specific biological role is not fully established.

Q: What does rs116092581 do to gene expression?

The alternate allele of rs116092581 is associated with reduced expression of LINC02609 specifically in esophageal muscularis (the muscular layer of the esophagus) tissue, based on GTEx data from 953 tissue donors. This type of variant is called an expression-quantitative trait locus, or eQTL.

Q: Is rs116092581 linked to any disease or health condition?

No specific disease or health associations for rs116092581 are documented in the available study sources. The variant has been examined in the context of a large UK Biobank biomarker study, but no specific findings for this variant are reported in that study.

Q: How reliable is the evidence for rs116092581?

Current evidence is limited to a single tissue-level gene expression effect in esophagus muscularis from GTEx (953 donors, p=3.1e-5, FDR < 0.05). This is preliminary and restricted to one tissue type, with no replication across other tissues in the available data.

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

An eQTL (expression-quantitative trait locus) is a genetic variant that affects how much a gene is expressed, or active, in a given tissue. For rs116092581, the finding means the alternate allele is associated with lower LINC02609 activity in esophageal muscle, though whether this has any functional or health consequence is not yet established.

rs116092581 (LINC02609): Esophageal Expression Variant

Key takeaways

rs116092581 sits near LINC02609, a non-coding RNA gene that regulates nearby genes without making protein
The alternate allele is linked to reduced LINC02609 activity in esophageal muscle tissue, based on expression data from 953 tissue donors
This variant was studied in the context of a large UK Biobank genome-wide biomarker study (363,228 participants)
Current evidence is limited to one tissue-level expression effect; no confirmed disease or biomarker associations are documented in the available sources

Key takeaways

rs116092581 sits near LINC02609, a non-coding RNA gene that regulates nearby genes without making protein
The alternate allele is linked to reduced LINC02609 activity in esophageal muscle tissue, based on expression data from 953 tissue donors
This variant was studied in the context of a large UK Biobank genome-wide biomarker study (363,228 participants)
Current evidence is limited to one tissue-level expression effect; no confirmed disease or biomarker associations are documented in the available sources

What the research says GTEx v11 eQTL (expression-quantitative trait locus) analysis across 953 tissue donors identifies a significant association between the alternate allele of rs116092581 and reduced expression of LINC02609 in esophagus muscularis tissue (effect slope -0.51 on log2-normalized scale, p=3.1e-5, FDR < 0.05) GTEx Portal. LINC02609 is a long intergenic non-coding RNA (lincRNA), a class of RNA molecule that does not produce protein but can modulate the activity of nearby genes. A genome-wide study of 35 blood and urine biomarkers in the UK Biobank (n=363,228) identified 1,857 loci associated with at least one of those traits, providing the population-scale research context for this genomic region.

Reported associations

LINC02609 expression, esophagus muscularis: The alternate allele is associated with reduced expression in this tissue (effect slope -0.51 on log2-normalized scale, p=3.1e-5, n=953 donors) GTEx Portal

Evidence quality The only documented association for rs116092581 in the available sources is a cis-eQTL effect on LINC02609 (a regulatory variant affecting expression of a gene in the immediate chromosomal neighborhood) in esophagus muscularis tissue, reaching FDR < 0.05 in GTEx v11 (p=3.1e-5, 953 donors) GTEx Portal. No other tissues reach significance in the available data, suggesting a tissue-restricted signal. The UK Biobank genome-wide biomarker study (n=363,228, Bonferroni-corrected threshold p < 5x10-9) identified 1,857 loci across 35 traits; no specific biomarker effect sizes for this variant are reported in that study. The overall evidence base is therefore preliminary and restricted to a single tissue-level expression signal that has not been replicated across tissue types in the available data.

Tissue-specific expression effects

LINC02609: Reduced expression in esophagus muscularis tissue with the alternate allele (eQTL slope -0.51, p=3.1e-5); no other tissues show significant effects in the available data GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is the LINC02609 gene?

LINC02609 is a long intergenic non-coding RNA (lincRNA), a type of RNA molecule that does not produce protein but can influence the activity of nearby genes. Its specific biological role is not fully established.

What does rs116092581 do to gene expression?

The alternate allele of rs116092581 is associated with reduced expression of LINC02609 specifically in esophageal muscularis (the muscular layer of the esophagus) tissue, based on GTEx data from 953 tissue donors. This type of variant is called an expression-quantitative trait locus, or eQTL.

Is rs116092581 linked to any disease or health condition?

No specific disease or health associations for rs116092581 are documented in the available study sources. The variant has been examined in the context of a large UK Biobank biomarker study, but no specific findings for this variant are reported in that study.

How reliable is the evidence for rs116092581?

Current evidence is limited to a single tissue-level gene expression effect in esophagus muscularis from GTEx (953 donors, p=3.1e-5, FDR < 0.05). This is preliminary and restricted to one tissue type, with no replication across other tissues 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 that affects how much a gene is expressed, or active, in a given tissue. For rs116092581, the finding means the alternate allele is associated with lower LINC02609 activity in esophageal muscle, though whether this has any functional or health consequence is not yet established.

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