Expressive

rs10841414 (TCP1P3/LINC02468): Cardiac eQTL Variant

Key takeaways

  • Rs10841414 near TCP1P3 and LINC02468 was identified in a GWAS of 153,950 Korean adults spanning 36 quantitative traits.
  • The alternate allele reduces expression of one nearby gene in testis, aorta, tibial artery, and lung.
  • The same alternate allele increases expression of a second nearby gene in heart left ventricle and atrial tissue.
  • Evidence is from a single East Asian cohort with no independent replication reported for this specific variant.
  • Effect sizes on gene expression are modest and functional consequences remain unclear.

Key takeaways

  • Rs10841414 is located near TCP1P3 (a pseudogene, meaning a non-functional copy of a gene) and LINC02468 (a long intergenic non-coding RNA, a type of regulatory RNA molecule), and was identified in a large genome-wide association study (GWAS) of the Korean population.
  • The alternate allele at this variant is linked to reduced expression of a nearby gene (ENSG00000255910) in testis, aortic artery, tibial artery, and lung tissue.
  • The same alternate allele is linked to increased expression of a second nearby gene (ENSG00000302733) in heart left ventricle and atrial tissue.
  • All association evidence comes from a single large East Asian cohort; independent replication for this specific variant has not been described in the provided sources.
  • Both expression effects are modest in size and their functional consequences are not yet established.

What the research says A GWAS of 153,950 Korean adults in the KCPS2 Biobank analyzed 36 quantitative traits and identified hundreds of previously unreported genetic loci across the genome. GTEx eQTL (expression quantitative trait locus) analysis shows the alternate allele at rs10841414 is associated with reduced expression of ENSG00000255910 in testis, aorta, tibial artery, and lung, and with increased expression of ENSG00000302733 in heart left ventricle and atrial tissue GTEx Portal.

Reported associations

  • Quantitative traits in Korean adults: Rs10841414 was identified as a locus of interest in a GWAS of 36 quantitative traits (including cardiovascular, metabolic, and hematological traits) across 153,950 participants; the specific trait mapped to this variant is not detailed in the provided study text.
  • Gene expression - ENSG00000255910 (testis, arteries, lung): The alternate allele is associated with reduced expression in testis (log2 slope -0.29), aorta (-0.20), tibial artery (-0.17), and lung (-0.13) GTEx Portal.
  • Gene expression - ENSG00000302733 (heart): The alternate allele is associated with increased expression in heart left ventricle (+0.23) and heart atrial appendage (+0.20) GTEx Portal.

Evidence quality The primary GWAS evidence derives from a single large Korean cohort of 153,950 individuals, which is well powered for common variant discovery but lacks independent replication specifically for rs10841414 in the provided sources. The study used a linear mixed model (SAIGE) with controls for population stratification (median lambda GC 1.23, median S-LDSC intercept 1.04). The eQTL data from GTEx v11 (953 donors, FDR less than 0.05) provides corroborating mechanistic evidence GTEx Portal, with p-values across all eQTL associations ranging from 3.2e-9 (tibial artery) to 8.1e-5 (heart atrial appendage). No conflicting findings are present in the provided sources, but the absence of independent replication means all findings should be considered preliminary.

Tissue-specific expression effects

  • ENSG00000255910: The alternate allele is associated with reduced expression in testis, aorta, tibial artery, and lung, with the largest magnitude effect observed in testis GTEx Portal.
  • ENSG00000302733: The alternate allele is associated with increased expression in heart left ventricle and heart atrial appendage GTEx Portal.

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs10841414?

Rs10841414 is a single nucleotide polymorphism (a one-letter DNA change) located near the TCP1P3 pseudogene and the LINC02468 non-coding RNA. It was identified in a large Korean population genome-wide association study of 153,950 adults.

What is TCP1P3?

TCP1P3 is a pseudogene, meaning a DNA sequence that resembles a functional gene but does not produce a working protein. It sits in the same genomic region as LINC02468, a regulatory RNA molecule.

What is LINC02468?

LINC02468 is a long intergenic non-coding RNA, meaning it is transcribed from DNA but does not encode a protein. Non-coding RNAs like LINC02468 often play regulatory roles in gene expression.

Is rs10841414 linked to heart disease?

GTEx eQTL data shows the alternate allele at rs10841414 is associated with altered gene expression in heart muscle tissue. No direct link to heart disease has been reported in the provided sources; these expression effects are a potential biological mechanism, not a clinical finding.

How reliable is the evidence for rs10841414?

Evidence comes from a single large Korean cohort study (153,950 participants) and GTEx expression data from 953 donors. Independent replication for this specific variant has not been described in the provided sources, so findings should be considered preliminary.