Expressive

rs10489631 (C1orf141): Lung Expression eQTL Variant

Key takeaways

  • Carriers of the alternate allele show increased C1orf141 expression in the lung and reduced SLC35D1 expression in the stomach, brain, and skin.
  • The stomach effect on SLC35D1 is among the strongest signals at this locus (p=1.4e-22 in GTEx v11, 953 donors).
  • A second uncharacterized gene (ENSG00000275678) shows increased expression in both the brain hypothalamus and the lung from the same allele.
  • All current evidence comes from tissue expression studies, with no direct links to disease outcomes in the provided literature.
  • SGIP1 expression in testis tissue is also elevated by the alternate allele, expanding the variant's multi-tissue footprint.

Key takeaways

  • Carriers of the alternate allele show increased C1orf141 expression in the lung and reduced SLC35D1 expression in the stomach, brain, and skin.
  • The stomach effect on SLC35D1 is among the strongest signals at this locus (p=1.4e-22 in GTEx v11, 953 donors).
  • A second uncharacterized gene (ENSG00000275678) shows increased expression in both the brain hypothalamus and the lung from the same allele.
  • All current evidence comes from tissue expression studies, with no direct links to disease outcomes in the provided literature.
  • SGIP1 expression in testis tissue is also elevated by the alternate allele, expanding the variant's multi-tissue footprint.

What the research says GTEx v11, a large-scale tissue expression reference covering 953 human donors, identifies rs10489631 as a cis-eQTL (a variant that alters the expression of physically nearby genes) affecting at least four genes across multiple tissues GTEx Portal. The alternate allele is associated with increased C1orf141 expression in lung (p=6.4e-15) and with reduced SLC35D1 expression in the stomach at particularly high statistical confidence (p=1.4e-22) GTEx Portal. Two provided clinical studies - one on host genetics and the airway microbiome in chronic obstructive pulmonary disease, and one on gene-by-serum-urate interactions for bone mineral density - do not report associations for rs10489631 specifically, so no GWAS-level disease trait links appear in the provided evidence base.

Reported associations

  • C1orf141 expression (lung): The alternate allele is linked to increased expression of C1orf141 in lung tissue GTEx Portal
  • SLC35D1 expression (stomach): The alternate allele is linked to reduced expression of SLC35D1 in the stomach, the strongest single-tissue effect at this locus GTEx Portal
  • SLC35D1 expression (brain): The alternate allele is linked to reduced SLC35D1 expression in the nucleus accumbens, a structure in the brain's basal ganglia GTEx Portal
  • SLC35D1 expression (skin): The alternate allele is linked to reduced SLC35D1 expression in both sun-exposed skin of the lower leg and non-sun-exposed skin of the suprapubic region GTEx Portal
  • ENSG00000275678 expression (brain): The alternate allele is linked to increased expression of this uncharacterized gene in the brain hypothalamus GTEx Portal
  • ENSG00000275678 expression (lung): The alternate allele is linked to increased expression of this locus in lung tissue GTEx Portal
  • SGIP1 expression (testis): The alternate allele is linked to increased expression of SGIP1 in testis GTEx Portal

Evidence quality All reported associations for rs10489631 in the provided literature derive from eQTL data in GTEx v11 (953 donors), not from genome-wide association studies linking this variant to clinical disease outcomes or measurable health phenotypes GTEx Portal. An eQTL association establishes that a variant influences gene expression levels, which is one step in a potential causal chain but does not on its own establish clinical relevance. Statistical confidence varies across the signals: the SLC35D1 stomach effect reaches p=1.4e-22 while the SGIP1 testis effect sits at p=8.1e-5, though all reported signals pass the GTEx FDR threshold of 0.05. The two provided clinical studies - covering airway microbiome genetics in COPD and gene-by-environment interactions for bone mineral density - do not report rs10489631 associations, leaving the variant's clinical significance unestablished in the provided evidence base.

Tissue-specific expression effects

  • C1orf141: Increased expression in lung tissue in carriers of the alternate allele GTEx Portal
  • SLC35D1: Reduced expression in the stomach (p=1.4e-22), in the nucleus accumbens of the brain (p=1.5e-5), and in both sun-exposed (p=2.5e-5) and non-sun-exposed skin (p=9.0e-5) GTEx Portal
  • ENSG00000275678: Increased expression in the brain hypothalamus (p=4.2e-5) and in lung (p=9.8e-9) GTEx Portal
  • SGIP1: Increased expression in testis (p=8.1e-5) GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs10489631?

rs10489631 is a single nucleotide polymorphism (a one-letter change in the DNA sequence) located near the C1orf141 gene on chromosome 1. It has been identified as an expression quantitative trait locus (eQTL), meaning it influences how much of several nearby genes are produced in different body tissues.

What genes does rs10489631 affect?

Based on GTEx v11 tissue expression data from 953 donors, rs10489631 influences the expression of four genes: C1orf141 in lung, SLC35D1 in stomach, brain, and skin, an uncharacterized transcript (ENSG00000275678) in the brain hypothalamus and lung, and SGIP1 in testis.

Is rs10489631 associated with any disease?

The provided research does not establish a direct link between rs10489631 and any clinical disease. The available evidence shows only tissue-specific changes in gene expression levels, which are one step removed from disease outcomes.

What does C1orf141 do?

C1orf141 stands for chromosome 1 open reading frame 141. Its specific biological function is not well characterized in the provided research. The alternate allele of rs10489631 is associated with increased C1orf141 expression specifically in lung tissue.

What is SLC35D1 and why does rs10489631 affect it?

SLC35D1 encodes a protein involved in transporting sugar molecules across cell membranes. rs10489631 is associated with reduced SLC35D1 expression in the stomach, brain, and skin, though the downstream biological consequences of this reduction are not described in the provided evidence.