Expressive

rs1203930 (LNCNEF): Thyroid Gene Expression Variant

Key takeaways

  • rs1203930 is near LNCNEF (also called LINC01747), a long non-coding RNA gene.
  • The alternate allele is linked to increased expression of three genes in thyroid tissue: LNCNEF, FOXA2, and LINC00261.
  • The thyroid expression signals are statistically very strong, with p-values as low as 2.2e-49 across 953 donors.
  • These are gene expression (eQTL) effects, not directly validated disease associations.
  • This locus appears in large multi-population genetic studies covering over 600,000 participants.

Key takeaways

  • rs1203930 is a genetic variant near the LNCNEF gene (also known as LINC01747), a long non-coding RNA.
  • The alternate allele is linked to increased expression of three genes in thyroid tissue: LNCNEF, FOXA2, and LINC00261.
  • The thyroid expression signals are statistically very strong, with p-values as low as 2.2e-49 across 953 donors.
  • These are gene expression (eQTL) effects, not directly validated clinical disease associations.
  • This locus has been catalogued in large multi-population genetic studies covering over 600,000 participants.

What the research says rs1203930 maps to the LNCNEF locus (also catalogued as LINC01747, a long intergenic non-coding RNA) and has been included in large multi-population genome-wide association studies, among them one of 635,969 VA Million Veteran Program participants across 2,068 traits and a cross-population atlas of 220 phenotypes in BioBank Japan (n=179,000) with meta-analyses spanning the UK Biobank and FinnGen (total n approximately 628,000). GTEx v11 expression-quantitative trait locus (eQTL) analysis of 953 donors identifies the alternate allele as strongly associated with increased expression of LNCNEF (slope +0.54, p=2.2e-49), FOXA2 (slope +0.47, p=3.9e-46), and LINC00261 (slope +0.36, p=2.1e-16), all specifically in thyroid tissue GTEx Portal.

Reported associations

  • LNCNEF thyroid expression (eQTL): The alternate allele is associated with increased expression of this gene in thyroid tissue (slope +0.54, p=2.2e-49, GTEx v11, n=953 donors) GTEx Portal
  • FOXA2 thyroid expression (eQTL): The alternate allele is associated with increased expression of FOXA2 in thyroid tissue (slope +0.47, p=3.9e-46, GTEx v11, n=953 donors) GTEx Portal
  • LINC00261 thyroid expression (eQTL): The alternate allele is associated with increased expression of LINC00261 in thyroid tissue (slope +0.36, p=2.1e-16, GTEx v11, n=953 donors) GTEx Portal

Evidence quality All three thyroid eQTL signals for this locus pass a stringent false discovery rate (FDR) threshold in GTEx v11 (953 donors), with p-values ranging from 2.1e-16 to 2.2e-49 GTEx Portal. The eQTL effects are thyroid-specific in the provided data, with no other tissues reported. The two large GWAS studies that include this genomic region enrolled diverse populations, including individuals genetically similar to African, Admixed American, East Asian, and European reference groups, which increases potential generalizability of findings in this region. Specific disease or phenotype associations for rs1203930 are not detailed in the provided study excerpts, and eQTL effects represent gene-expression mechanism rather than directly replicated clinical outcomes; evidence for clinical interpretation should be considered preliminary.

Tissue-specific expression effects

  • LNCNEF: Increased expression in thyroid tissue in carriers of the alternate allele GTEx Portal
  • FOXA2: Increased expression in thyroid tissue in carriers of the alternate allele GTEx Portal
  • LINC00261: Increased expression in thyroid tissue in carriers of the alternate allele GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs1203930?

rs1203930 is a single-nucleotide variant located near the LNCNEF gene, also known as LINC01747. It has been catalogued in large-scale multi-population genome-wide association studies and shows strong associations with gene expression in thyroid tissue.

What does the LNCNEF gene do?

LNCNEF, also called LINC01747, is a long intergenic non-coding RNA - a type of gene that produces RNA molecules but is not translated into protein. The specific biological function of LNCNEF is not described in the studies reviewed for this entry.

Which tissues does rs1203930 affect?

GTEx v11 data from 953 donors shows that rs1203930 affects gene expression specifically in thyroid tissue. The alternate allele is associated with increased expression of LNCNEF, FOXA2, and LINC00261 in this tissue.

How strong is the evidence for rs1203930?

The eQTL evidence is statistically very strong, with p-values ranging from 2.1e-16 to 2.2e-49 in 953 donors from GTEx v11. These are gene expression effects rather than disease associations, and specific clinical implications are not established in the studies provided.

Is rs1203930 linked to any diseases?

The studies provided do not report specific disease associations for rs1203930. The primary documented signal is its effect on gene expression in thyroid tissue. Broader associations may exist in larger databases but are not confirmed in the materials reviewed here.