rs11163801 (LINC01725): eQTL Across Skin and Thyroid
Key takeaways
- rs11163801 sits in LINC01725, a non-coding RNA gene that regulates other genes without producing a protein
- The alternative allele raises LINC01725 expression in five tissues: non-sun-exposed skin, thyroid, pancreas, sun-exposed skin, and aortic artery
- GTEx data from 953 donors shows statistically strong signals, with thyroid (p=1.8e-11) and non-sun-exposed skin (p=2.4e-9) being the most significant
- This locus appeared in a metabolomics GWAS of 217 plasma metabolites in 2,076 Framingham Heart Study participants
- The functional meaning of altered LINC01725 expression and its health relevance are not yet established
Key takeaways
- rs11163801 sits in LINC01725, a non-coding RNA gene that regulates other genes without producing a protein
- The alternative allele raises LINC01725 expression in five tissues: non-sun-exposed skin, thyroid, pancreas, sun-exposed skin, and aortic artery
- GTEx data from 953 donors shows statistically strong signals, with thyroid (p=1.8e-11) and non-sun-exposed skin (p=2.4e-9) being the most significant
- This locus appeared in a metabolomics GWAS of 217 plasma metabolites in 2,076 Framingham Heart Study participants
- The functional meaning of altered LINC01725 expression and its health relevance are not yet established
What the research says A genome-wide association study (GWAS) of 217 plasma metabolites in 2,076 participants of the Framingham Heart Study identified 31 genetic loci associated with circulating metabolite levels, including 23 not previously reported; heritability (the proportion of trait variation explained by inherited factors) accounted for more than 20% of inter-individual metabolite variation in 66% of analytes measured PMID 24703692. Expression quantitative trait locus (eQTL) analysis from GTEx v11, encompassing 953 donors with cis-window associations at FDR<0.05, shows that the alternative allele at this locus consistently raises LINC01725 expression across five tissues, with the thyroid signal at p=1.8e-11 and the non-sun-exposed skin signal at p=2.4e-9 GTEx Portal.
Reported associations
- Plasma metabolite levels: rs11163801 was identified among 31 loci in a GWAS of 217 plasma metabolites in 2,076 community-based Framingham Heart Study participants; the specific metabolite associated with this locus is not specified in the available study text PMID 24703692
- LINC01725 expression - non-sun-exposed skin: the alternative allele is associated with increased expression in suprapubic (non-sun-exposed) skin (slope +0.24, p=2.4e-9, 953 GTEx donors) GTEx Portal
- LINC01725 expression - thyroid: the alternative allele is associated with increased expression in thyroid tissue (slope +0.22, p=1.8e-11) GTEx Portal
- LINC01725 expression - pancreas: the alternative allele is associated with increased expression in pancreas tissue (slope +0.22, p=3.3e-5) GTEx Portal
- LINC01725 expression - sun-exposed skin: the alternative allele is associated with increased expression in sun-exposed lower leg skin (slope +0.18, p=1.4e-6) GTEx Portal
- LINC01725 expression - aortic artery: the alternative allele is associated with increased expression in the aorta (slope +0.15, p=8.8e-5) GTEx Portal
Evidence quality The metabolomics GWAS providing context for rs11163801 enrolled 2,076 Framingham Heart Study participants and used liquid chromatography-mass spectrometry to survey 217 plasma metabolites, identifying 31 genome-wide significant loci PMID 24703692. That study found that 93% of metabolites were explained by measured clinical factors at 20% or less, while heritability exceeded 20% for 66% of metabolites, underscoring the outsized genetic contribution to circulating metabolite variation. The specific metabolite associated with rs11163801 is not specified in the available study text, which limits interpretation of that signal. The GTEx eQTL data draws on 953 donors at FDR<0.05 and shows uniformly positive directional effects (that is, increased expression) across all five tissues; two signals fall below p=1e-8, providing the strongest statistical confidence for the thyroid and non-sun-exposed skin findings GTEx Portal. LINC01725 encodes a long intergenic non-coding RNA (lincRNA), a class of gene whose functional consequences are often incompletely characterized, and no downstream health or disease implications are established by the available evidence.
Tissue-specific expression effects
- LINC01725: the alternative allele is associated with increased expression in non-sun-exposed suprapubic skin, thyroid, pancreas, sun-exposed lower leg skin, and aortic artery tissue; all five tissue associations point in the same direction (increased expression) and are statistically significant in GTEx v11 data (953 donors, FDR<0.05) GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is the LINC01725 gene?
LINC01725 is a long intergenic non-coding RNA (lincRNA) gene, meaning it produces an RNA molecule that is not converted into a protein. Non-coding RNAs are thought to help regulate nearby gene activity, though the specific biological function of LINC01725 is not yet well characterized.
What does rs11163801 do to gene expression?
GTEx expression data from 953 donors shows that the alternative allele at rs11163801 is associated with higher LINC01725 expression across five tissues, including skin, thyroid, pancreas, and aortic artery. What this increased expression means for health outcomes has not been established.
Which tissues are affected by rs11163801?
GTEx v11 data identifies five tissues where this variant raises LINC01725 expression: non-sun-exposed suprapubic skin, thyroid, pancreas, sun-exposed lower leg skin, and aortic artery. The thyroid and non-sun-exposed skin signals are statistically the strongest.
Is rs11163801 linked to any diseases or health conditions?
This variant has been identified in a genome-wide study of circulating metabolite levels in the Framingham Heart Study, and shows expression effects in multiple tissues. However, the available evidence does not establish a direct link to any specific disease or health condition.
What is an eQTL and why does it matter for rs11163801?
An eQTL (expression quantitative trait locus) is a genetic variant associated with differences in gene expression levels rather than directly with a disease or trait. For rs11163801, eQTL analysis shows consistent association with higher LINC01725 activity across five tissue types, which may point to a regulatory role, though downstream health effects are not yet known.