Expressive

rs11706153 (CELSR3): Gene Expression eQTL Variant

Key takeaways

  • rs11706153 sits near the CELSR3 gene and was studied in UK Biobank GWAS analyses covering up to 405,088 people
  • This variant reduces SHISA5 expression in esophagus and skin while simultaneously increasing WDR6 expression in those same tissues
  • CDC25A expression is increased in subcutaneous fat, and an unannotated gene is upregulated in visceral fat
  • Both GWAS studies used Bonferroni-corrected significance thresholds and replicated findings in independent cohorts
  • The eQTL effects span three tissue types, pointing to a regulatory rather than protein-coding mechanism

Key takeaways

  • rs11706153 sits near the CELSR3 gene and was examined in UK Biobank genome-wide association studies covering up to 405,088 people across blood and urine biomarkers and broad complex traits
  • GTEx v11 data from 953 donors show this variant reduces SHISA5 expression in esophagus and skin while simultaneously increasing WDR6 expression in those same tissues
  • The variant is also linked to increased CDC25A expression in subcutaneous fat and increased expression of an unannotated gene (ENSG00000285416) in visceral fat
  • Both studies used Bonferroni-corrected significance thresholds and replicated findings in independent cohorts
  • The eQTL effects span three tissue types, pointing to a regulatory rather than protein-coding mechanism for this locus

What the research says A genome-wide study of 35 blood and urine biomarkers in 363,228 UK Biobank individuals identified 1,857 loci with 3,374 fine-mapped associations, applying Bonferroni-corrected thresholds (p < 5 x 10^-9) across five ancestry groups. A separate analysis using the Quickdraws method, which combines a spike-and-slab prior on variant effects with stochastic variational inference and GPU acceleration, was applied to 405,088 UK Biobank participants across 79 quantitative and 50 binary traits, identifying 4.97% more associations than REGENIE and 22.71% more than FastGWA for quantitative traits, with findings replicated in Biobank Japan and FinnGen.

Reported associations

  • Blood and urine biomarkers (study scope): This locus falls within the scope of a systematic GWAS of 35 clinically measured serum and urine biomarkers in 363,228 UK Biobank participants, which identified 1,857 associated loci using fine-mapping across protein-altering, HLA, copy-number, and non-coding variants
  • Broad quantitative and binary traits (study scope): The region was included in a Quickdraws GWAS scan of 79 quantitative and 50 binary traits in 405,088 UK Biobank participants; specific trait-level associations for rs11706153 are not stated in the available study text

Evidence quality Both studies drew on large UK Biobank cohorts (n = 363,228 and n = 405,088), providing substantial genome-wide statistical power. The biomarker study performed meta-analysis across five ancestry groups (White British, non-British White, African, South Asian, and East Asian) and reported LD Score regression intercepts of 0.999 to 1.137, indicating well-controlled population stratification. The Quickdraws study validated results in Biobank Japan and FinnGen replication cohorts. Specific effect sizes and p-values for rs11706153 itself are not reported in the provided study text, so variant-level statistics cannot be confirmed from the available excerpts. The GTEx eQTL data (FDR < 0.05, 953 donors) provide the most directly variant-specific evidence available for this locus.

Tissue-specific expression effects

  • SHISA5: Reduced expression in esophagus mucosa, sun-protected skin (suprapubic), and sun-exposed skin (lower leg) GTEx Portal
  • WDR6: Increased expression in sun-protected skin (suprapubic), sun-exposed skin (lower leg), and esophagus mucosa GTEx Portal
  • ENSG00000285416 (unannotated gene): Increased expression in visceral (omental) adipose tissue GTEx Portal
  • CDC25A: Increased expression in subcutaneous adipose tissue GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs11706153 and where is it located?

rs11706153 is a genetic variant located near the CELSR3 gene. It has been examined in genome-wide association studies using UK Biobank data covering blood and urine biomarkers and broad complex traits across hundreds of thousands of participants.

What does rs11706153 do to gene expression?

GTEx v11 data from 953 donors show this variant reduces SHISA5 expression in esophageal and skin tissues while increasing WDR6 expression in those same tissues. It also increases CDC25A expression in subcutaneous fat and upregulates an unannotated gene in visceral fat.

What traits has rs11706153 been studied for?

Large UK Biobank analyses examined this region in studies of 35 blood and urine biomarkers (n=363,228) and a broad scan of 79 quantitative and 50 binary traits (n=405,088). Specific trait-level associations for this variant are not stated in the available study text.

What is an eQTL and why does it matter for this variant?

An eQTL, or expression quantitative trait locus, is a genetic variant that influences how much of a nearby gene is produced in a given tissue. For rs11706153, GTEx data show eQTL effects on at least four genes across skin, esophagus, and adipose tissue, suggesting this variant shapes biology through gene regulation.

Is rs11706153 linked to any diseases?

The studies providing context for this variant analyzed blood biomarkers and broad complex traits but do not report specific disease associations for rs11706153 in the available text. GTEx eQTL effects describe a regulatory mechanism, not a confirmed disease link.