Expressive

rs117470167 (HOXB-AS3/HOXB3): Brain and Heart eQTL

Key takeaways

  • rs117470167 is linked to increased expression of SP2-AS1 in two brain regions (the cerebellum and nucleus accumbens) as well as in skin and arterial tissue
  • The variant is also associated with reduced expression of MRPL10, a mitochondrial ribosome gene, in heart tissue
  • CDK5RAP3 expression in the hypothalamus and CBX1 expression in sun-exposed skin are both reduced by this variant
  • All four expression associations meet a false discovery rate below 5% in GTEx v11 data from 953 donors
  • No direct disease association results for this specific variant appear in the provided published literature

Key takeaways

  • rs117470167 is linked to increased expression of SP2-AS1 in two brain regions (the cerebellum and nucleus accumbens) as well as in skin and arterial tissue
  • The variant is also associated with reduced expression of MRPL10, a mitochondrial ribosome subunit gene, in heart tissue
  • CDK5RAP3 expression in the hypothalamus and CBX1 expression in sun-exposed skin are both reduced by this variant
  • All four expression associations meet a false discovery rate below 5% in GTEx v11 data from 953 donors
  • No direct disease association results for this specific variant appear in the provided published literature

What the research says The single study in this evidence base (German CA et al., Genetic Epidemiology, 2020) presents an ordinal regression method for genome-wide association analyses and applies it to COPD severity and hypertension categories; the provided text does not report findings specific to rs117470167. Expression quantitative trait locus (eQTL) data from GTEx v11 - based on 953 donors, a cis-window analysis, and a false discovery rate below 5% - identifies this variant as a regulatory locus affecting the activity of four genes across brain, cardiac, arterial, and skin tissues GTEx Portal. All reported associations are at the gene-expression level, with no disease outcome data available from the provided sources.

Reported associations

  • SP2-AS1 expression (brain, skin, and arteries): The alternative allele is associated with increased SP2-AS1 expression in the cerebellum (slope +0.81), nucleus accumbens (slope +0.66), non-sun-exposed skin (slope +0.44), tibial artery (slope +0.40), and aorta (slope +0.38), with nominal p-values from 2.2 x 10^-4 to 7.0 x 10^-7 across these five tissues GTEx Portal
  • MRPL10 expression (heart): The alternative allele is associated with reduced MRPL10 expression in the heart atrial appendage (slope -0.36, p = 1.1 x 10^-6); MRPL10 encodes a subunit of the mitochondrial ribosome, the cellular machinery that synthesizes proteins inside the mitochondria GTEx Portal
  • CDK5RAP3 expression (hypothalamus): The alternative allele is associated with reduced CDK5RAP3 expression in the hypothalamus (slope -0.45, p = 5.9 x 10^-5) GTEx Portal
  • CBX1 expression (skin): The alternative allele is associated with reduced CBX1 expression in sun-exposed lower-leg skin (slope -0.24, p = 4.7 x 10^-6) GTEx Portal

Evidence quality The available published study (German CA et al., Genetic Epidemiology, 2020; no PMID in source data) is a statistical methods paper that does not include association results for rs117470167, leaving direct genome-wide association study disease evidence absent from this entry. GTEx v11 eQTL data is drawn from 953 donors with all four reported associations passing FDR < 0.05; nominal p-values span 2.2 x 10^-4 to 7.0 x 10^-7, and effect sizes on a log2-normalized expression scale range from -0.45 (CDK5RAP3 in hypothalamus, reduced expression) to +0.81 (SP2-AS1 in cerebellum, increased expression) per copy of the alternative allele. No replication studies, disease outcome data, or conflicting findings are present in the provided sources, and the expression associations represent preliminary mechanistic evidence only.

Tissue-specific expression effects

  • SP2-AS1: Increased expression in five tissues - the cerebellum (slope +0.81, p = 1.5 x 10^-5), nucleus accumbens (slope +0.66, p = 2.2 x 10^-5), non-sun-exposed skin (slope +0.44, p = 7.0 x 10^-7), tibial artery (slope +0.40, p = 8.9 x 10^-7), and aorta (slope +0.38, p = 2.2 x 10^-4) GTEx Portal
  • MRPL10: Reduced expression in the heart atrial appendage (slope -0.36, p = 1.1 x 10^-6) GTEx Portal
  • CDK5RAP3: Reduced expression in the hypothalamus (slope -0.45, p = 5.9 x 10^-5) GTEx Portal
  • CBX1: Reduced expression in sun-exposed lower-leg skin (slope -0.24, p = 4.7 x 10^-6) GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Lifestyle context

Concrete actions anchored to the cited research. We do not prescribe, we describe.

Diet

  • DASH diet or salt-reduced diet for hypertension prevention Moderate

    Dietary modifications are evidence-based interventions for hypertension; genetic predisposition strengthens rationale for consistent implementation

    Consider DASH diet pattern: emphasize fruits, vegetables, whole grains, lean proteins, and limit sodium

Discuss with your doctor

  • cardiovascular risk assessment and prevention planning Moderate

    Hypertension association (PMID 31879980, p=2e-9) warrants discussion of family history, BP targets, and personalized prevention

    Schedule visit to review hypertension risk factors and preventive strategies

Exercise

  • regular aerobic exercise for cardiovascular health Moderate

    Exercise is effective for hypertension management and cardiovascular disease prevention, with enhanced benefit given genetic risk

    Aim for 150 minutes per week of moderate-intensity aerobic exercise or equivalent

Screening

  • blood pressure screening and monitoring Moderate

    rs117470167 shows strong association with hypertension risk (GWAS p=2e-9, n=185,568), indicating genetic predisposition

    Baseline blood pressure screening; annual monitoring, or more frequently if any elevation detected

Frequently asked questions

What does rs117470167 do?

rs117470167 is a genetic variant near the HOXB-AS3 and HOXB3 genes that affects how much nearby genes are expressed in specific tissues. In GTEx data from 953 donors, it is linked to higher SP2-AS1 activity in brain and arterial tissue and lower activity of other genes in the heart, hypothalamus, and skin.

What genes does rs117470167 affect?

According to GTEx v11 eQTL data, rs117470167 is associated with increased expression of SP2-AS1 across five tissues (two brain regions, one skin region, and two arteries), and with decreased expression of MRPL10 in heart tissue, CDK5RAP3 in the hypothalamus, and CBX1 in sun-exposed skin.

Is rs117470167 linked to any disease?

The available published study does not report disease association results for this specific variant. All current evidence is limited to gene-expression associations from GTEx eQTL data and does not establish a link to any clinical outcome.

Where in the genome is rs117470167?

rs117470167 is located at the HOXB-AS3 and HOXB3 locus, as identified by its rsID annotation in genome databases.

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

An eQTL (expression quantitative trait locus) is a genetic variant that influences how actively a nearby gene is expressed in a given tissue. rs117470167 is an eQTL for four genes across multiple tissues, suggesting it plays a role in regulating gene activity in brain, cardiac, arterial, and skin biology, although how those expression differences connect to health outcomes is not established from the available evidence.