Expressive

rs117838666 (SPACA6): Gene Expression Variant

Key takeaways

  • rs117838666 is linked to increased SPACA6 gene activity in whole blood
  • The same variant also increases NKG7 expression in esophageal muscle tissue
  • Evidence comes from GTEx v11 tissue expression data across 953 donors
  • No clinical or disease associations are established in current sources
  • This variant was identified in the context of large-scale UK Biobank genomic analysis

Key takeaways

  • rs117838666 is a DNA variant located near the SPACA6 gene that influences how actively this gene is read in whole blood
  • The same variant also increases activity of the NKG7 gene in esophageal muscle tissue
  • Both effects were identified in the GTEx v11 dataset spanning 953 tissue donors
  • No disease or clinical associations are documented in current sources for this variant
  • Evidence is preliminary and limited to gene expression, with no independent replication reported

What the research says GTEx v11 data, drawn from 953 donors across multiple tissue types, identifies rs117838666 as a cis-eQTL (a variant that alters the activity level of a nearby gene) for SPACA6: the alternative allele is associated with higher SPACA6 expression in whole blood (expression slope +0.48, p=6.1x10-5) GTEx Portal. The same allele also increases NKG7 expression in esophageal muscularis, the muscular outer layer of the esophagus (expression slope +0.68, p=4.4x10-5) GTEx Portal. A 2025 Nature Genetics study by Loya et al. applied the Quickdraws mixed-model GWAS method to 13.3 million variants in 405,088 UK Biobank participants across 79 quantitative and 50 binary traits, providing methodological context for large-scale variant discovery that encompasses this locus.

Reported associations

  • SPACA6 gene expression (Whole Blood): The alternative allele is associated with increased SPACA6 expression (expression slope +0.48; p=6.1x10-5) GTEx Portal
  • NKG7 gene expression (Esophagus Muscularis): The alternative allele is associated with increased NKG7 expression (expression slope +0.68; p=4.4x10-5) GTEx Portal

Evidence quality Association evidence for rs117838666 is currently limited to eQTL data from GTEx v11 (953 donors, FDR<0.05 discovery threshold). The p-values for both signals, 6.1x10-5 for SPACA6 in whole blood and 4.4x10-5 for NKG7 in esophageal muscularis, meet the FDR-controlled threshold but fall short of the genome-wide significance threshold (typically p<5x10-8) GTEx Portal. No replication in independent cohorts, no functional validation studies, and no trait-level associations with disease or clinical outcomes are reported in the provided sources. The Quickdraws UK Biobank GWAS (Loya et al., 2025, n=405,088) establishes the analytical framework for large-scale variant discovery but does not specifically report phenotypic associations for this variant.

Tissue-specific expression effects

  • SPACA6: the alternative allele is associated with increased expression in whole blood GTEx Portal
  • NKG7: the alternative allele is associated with increased expression in esophageal muscularis (the outer muscle layer of the esophagus) GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs117838666?

rs117838666 is a single nucleotide polymorphism (a one-letter change in the DNA sequence) located near the SPACA6 gene. It is classified as an expression quantitative trait locus, meaning it influences how much of a gene is produced in specific tissues.

What does rs117838666 do to SPACA6 gene expression?

In whole blood tissue, the alternative allele of rs117838666 is associated with higher SPACA6 gene expression, based on GTEx v11 data from 953 donors.

Does rs117838666 affect any genes other than SPACA6?

Yes. GTEx v11 data also shows that the alternative allele of this variant is associated with increased NKG7 gene expression in esophageal muscularis, the outer muscular layer of the esophagus.

Is rs117838666 linked to any diseases or health conditions?

No disease or clinical associations are documented in the sources available for this entry. The variant's known effects are limited to gene expression changes in specific tissues.

How strong is the evidence for rs117838666?

The evidence is preliminary. Both gene expression associations were identified in GTEx v11 under an FDR-controlled threshold, but have not been independently replicated or functionally validated in the sources reviewed here.