Expressive

rs116503681 (RAP1GAP): Blood Biomarker GWAS Variant

Key takeaways

  • rs116503681 was identified in a genome-wide scan of 35 blood and urine lab measurements in over 363,000 UK Biobank participants
  • The study used strict significance thresholds across more than 9 million variants and included multiple ancestry groups
  • The ALT allele is linked to higher LINC02596 gene expression in thyroid tissue, based on GTEx data from 953 donors
  • Specific biomarker trait associations and effect sizes are not detailed in the available evidence

Key takeaways

  • rs116503681 is a variant at the RAP1GAP locus, identified in a genome-wide study of 35 blood and urine laboratory measurements in up to 363,228 UK Biobank participants
  • The study used Bonferroni-corrected significance thresholds across more than 9 million genetic variants and included participants from multiple ancestry groups
  • The ALT allele of this variant is associated with increased expression of the LINC02596 gene in thyroid tissue, based on GTEx data from 953 donors
  • Specific biomarker associations and effect sizes for this variant are not detailed in the available study text; interpret with caution

What the research says A large genome-wide association study (GWAS, a method that scans large numbers of genetic variants across the genome to find those statistically linked to a trait) of 35 blood and urine laboratory measurements in UK Biobank (n=363,228) identified 1,857 genetic loci containing 3,374 fine-mapped associations, with variants at the RAP1GAP locus among those examined. The analysis covered multiple ancestry groups (White British n=318,953; non-British White n=23,582; African n=6,019; South Asian n=7,338; East Asian n=1,082) and applied a Bonferroni-corrected significance threshold of p less than 5 x 10^-9 for imputed variants across more than 9 million sites. GTEx v11 expression data (953 donors) shows that the ALT allele of rs116503681 is linked to increased expression of LINC02596 (a long intergenic non-coding RNA gene) in thyroid tissue (slope +0.36, p=1.2x10^-4) GTEx Portal.

Reported associations

  • Blood and urine biomarkers: This variant was identified in a systematic GWAS of 35 laboratory measurements in UK Biobank (n=363,228); the specific biomarker(s) most strongly linked to rs116503681 are not stated in the available study text
  • LINC02596 expression in thyroid tissue: The ALT allele is associated with increased expression of LINC02596 in thyroid tissue (slope +0.36, p=1.2x10^-4, FDR less than 0.05) GTEx Portal

Evidence quality The genome-wide study associated with this locus is large (primary n=363,228; meta-analysis n=355,891 across four ancestry groups) and used rigorous statistical controls, including Bonferroni correction across more than 9 million imputed variants and LD score regression (a method to control for population structure) with intercepts between 0.999 and 1.137 across all 35 phenotypes. However, specific details about rs116503681, including which of the 35 biomarkers it is associated with, its effect size, and whether the finding has been independently replicated, are not provided in the available study text. The GTEx eQTL (expression quantitative trait locus, meaning a variant statistically linked to gene expression levels) finding for LINC02596 in thyroid tissue meets FDR less than 0.05 significance in 953 donors, representing mechanistic evidence rather than a disease or clinical outcome association.

Tissue-specific expression effects

  • LINC02596: The ALT allele is associated with increased expression in thyroid tissue GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs116503681 associated with?

rs116503681 is at the RAP1GAP locus and was identified in a large genome-wide study of 35 blood and urine laboratory measurements in UK Biobank. The specific lab test it is most strongly linked to is not detailed in the available study text. It is also associated with higher LINC02596 gene expression in thyroid tissue based on GTEx data.

What does the GTEx data show for rs116503681?

GTEx (Genotype-Tissue Expression) data from 953 donors shows that people carrying the ALT allele of rs116503681 tend to have higher expression of the LINC02596 gene in thyroid tissue. This is a molecular mechanism finding and does not directly indicate a disease or clinical outcome.

How large was the study that found rs116503681?

The main study analyzed 363,228 individuals from UK Biobank across multiple ancestry groups, including White British, non-British White, African, South Asian, and East Asian participants, with a multi-ancestry meta-analysis of 355,891 individuals.

Is rs116503681 linked to thyroid disease?

No thyroid disease association is reported in the available evidence. The only thyroid-related finding is a GTEx signal showing the variant affects LINC02596 gene expression levels in thyroid tissue, which is a molecular observation rather than a disease diagnosis.

What is the RAP1GAP gene?

The available study text does not describe the function of RAP1GAP in detail. RAP1GAP is the gene locus where rs116503681 is located, and this variant was flagged in a large genome-wide study of blood and urine laboratory measurements.