rs117889339 (ARHGAP39): Biomarker Genetics Variant

Key takeaways

• GTEx eQTL data link this variant to increased expression of four genes across six tissue types: skeletal muscle, subcutaneous fat, tibial arteries, cerebellar brain tissue, breast, and stomach
• RECQL4 shows increased expression in cerebellar brain tissue, breast mammary tissue, and stomach when the alternate allele is present
• rs117889339 sits in the ARHGAP39 gene region and was captured in a genome-wide scan of 35 blood and urine biomarkers across 363,228 UK Biobank participants
• The specific biomarker this variant is linked to is not detailed in the available study excerpt

What the research says A genome-wide association study of 35 blood and urine biomarkers in the UK Biobank enrolled 363,228 individuals across five ancestry groups and identified 1,857 associated loci and 3,374 fine-mapped variant-biomarker associations. Using Mendelian Randomization (a statistical method that uses genetic variants to test whether one trait causally influences another), the same study established 51 causal relationships between biomarkers and diseases, including the previously recognized connections between urate and gout and between cystatin C and stroke. Separately, GTEx v11 data (953 donors, cis-window, FDR < 0.05) show the alternate allele at this locus is associated with increased expression of four genes across multiple tissue types GTEx Portal.

Reported associations

• Blood or urine biomarker (UK Biobank): A genome-wide study of 35 routine clinical measurements (n=363,228 individuals) includes this locus among its findings, but the available study text does not name which specific biomarker is linked to rs117889339 or report a per-variant effect size for this locus

Evidence quality The UK Biobank biomarker study used a Bonferroni-corrected significance threshold of p < 5 x 10^-9 for assayed and imputed variants, and polygenic risk findings were replicated in an independent FinnGen cohort (n=135,500). Linkage disequilibrium score regression intercepts across all 35 phenotypes ranged from 0.999 to 1.137, indicating well-controlled population stratification. The specific association and effect size for rs117889339 are not reported in the available study excerpt, which means the strength of evidence for this locus as a biomarker variant cannot be fully characterized from the provided text alone. GTEx eQTL findings (GTEx v11, 953 donors, FDR < 0.05) are independent of the biomarker GWAS and represent regulatory associations rather than disease or biomarker outcome data.

Tissue-specific expression effects

• ENSG00000254533: The alternate allele is linked to increased expression of this gene in tibial artery tissue and skeletal muscle GTEx Portal
• ENSG00000301017: The alternate allele is linked to increased expression in subcutaneous adipose tissue and skeletal muscle GTEx Portal
• RECQL4: The alternate allele is linked to increased expression in the cerebellar hemisphere of the brain, breast mammary tissue, and stomach GTEx Portal
• PPP1R16A: The alternate allele is linked to increased expression in laboratory-cultured immune cell lines (EBV-transformed lymphocytes, a standard GTEx cell model derived from white blood cells) GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.