rs12451696 (SLC47A1): Solute Carrier Gene Variant
Key takeaways
- rs12451696 is located near SLC47A1 (Solute Carrier Family 47 Member 1), a transporter gene in the solute carrier protein family.
- This variant was catalogued in a large genome-wide study of 35 blood and urine biomarkers in 363,228 UK Biobank participants.
- GTEx data show the variant increases SLC47A1 gene expression in brain putamen tissue but decreases it in cultured fibroblasts.
- Expression effects are also seen in testis, visceral fat, tibial nerve, and thyroid tissues across five gene targets.
- Specific biomarker association details for this variant are not available from the provided study text.
Key takeaways
- rs12451696 is located near SLC47A1 (Solute Carrier Family 47 Member 1), a transporter gene in the solute carrier protein family.
- This variant was catalogued in a large genome-wide study of 35 blood and urine biomarkers in 363,228 UK Biobank participants.
- GTEx data show the variant increases SLC47A1 gene expression in brain putamen tissue but decreases it in cultured fibroblasts, with opposite directional effects in the two tissues.
- Expression effects are also seen in testis, visceral fat, tibial nerve, and thyroid tissues across five gene targets.
- Specific biomarker association details for this variant are not available from the provided study text.
What the research says A genome-wide association study of 35 blood and urine biomarkers in 363,228 UK Biobank participants identified 1,857 loci associated with at least one measured trait, applying a Bonferroni-corrected significance threshold of p < 5 x 10^-9 for imputed variants, with findings validated against 42 previously published cohorts; the study also applied Mendelian Randomization across 40 medically relevant phenotypes, identifying 51 causal relationships including urate effects on gout and cystatin C effects on stroke, though the provided text does not enumerate specific association statistics for this locus. GTEx v11 eQTL data (953 donors, FDR < 0.05) link rs12451696 to opposing expression effects at this locus - increased in brain putamen basal ganglia (slope +0.29, p=3.5e-5) and decreased in cultured fibroblasts (slope -0.25, p=2.6e-8) GTEx Portal.
Reported associations
- Blood and urine biomarkers (trait unspecified): This variant was identified in the context of a genome-wide study of 35 blood and urine biomarkers across 363,228 UK Biobank participants; the provided text does not name the specific biomarker(s) or report effect sizes for this locus.
- SLC47A1 expression in brain putamen basal ganglia: The ALT allele is associated with increased expression of this gene (slope +0.29, p=3.5e-5) GTEx Portal.
- SLC47A1 expression in cultured fibroblasts: The ALT allele is associated with decreased expression of this gene (slope -0.25, p=2.6e-8) GTEx Portal.
Evidence quality The UK Biobank GWAS was conducted with Bonferroni-corrected significance thresholds in 363,228 participants across five population groups (meta-analysis n up to 355,891 individuals), with results cross-validated against 42 external cohorts, reflecting rigorous large-scale discovery methodology. However, the provided text does not include specific p-values, effect sizes, or beta coefficients for this locus individually, and no independent replication for rs12451696 specifically is described in the available excerpt. GTEx eQTL data are based on 953 donors using FDR < 0.05 correction; eQTL associations describe gene expression regulation rather than clinical outcomes, and the opposing tissue-specific expression directions (brain putamen vs. fibroblasts) should be treated as preliminary mechanistic signals. The presence of expression effects across five gene targets and multiple tissues broadens the mechanistic picture but does not establish clinical relevance for any specific outcome.
Tissue-specific expression effects
- SLC47A1: Increased expression in brain putamen basal ganglia and decreased expression in cultured fibroblasts - the ALT allele drives opposite directional effects in these two tissue types GTEx Portal.
- SNORD3B-2: Increased expression in testis tissue (slope +0.29, p=7.8e-5) GTEx Portal.
- ENSG00000279825: Increased expression in visceral adipose tissue (omentum, slope +0.19, p=3.8e-5) and tibial nerve (slope +0.19, p=2.2e-4) GTEx Portal.
- ENSG00000290544: Decreased expression in thyroid (slope -0.19, p=9.7e-5) and tibial nerve (slope -0.18, p=1.9e-5) GTEx Portal.
- ENSG00000262319: Decreased expression in thyroid tissue (slope -0.18, p=1.3e-4) GTEx Portal.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is the SLC47A1 gene?
SLC47A1 stands for Solute Carrier Family 47 Member 1. It belongs to the solute carrier transporter family, which encodes proteins responsible for moving substances across cell membranes in the body.
What does the rs12451696 variant do?
Based on GTEx expression data from 953 donors, rs12451696 is linked to altered SLC47A1 gene activity in a tissue-specific way. In brain putamen tissue the variant is associated with increased gene expression, while in cultured fibroblasts (lab-grown skin cells) it is associated with decreased expression.
Is rs12451696 linked to any disease or blood test result?
This variant was studied in a genome-wide analysis of 35 blood and urine biomarkers in 363,228 UK Biobank participants. The specific biomarker or health outcome associated with this locus is not detailed in the available study text.
What is an eQTL and why does it matter for this variant?
An eQTL (expression quantitative trait locus) is a genetic variant associated with differences in how much of a specific gene is produced in a given tissue. For rs12451696, it acts as an eQTL for SLC47A1 in brain and fibroblast tissue, meaning people with different versions of this variant tend to produce different amounts of the SLC47A1 protein in those specific locations.
Was rs12451696 studied across diverse populations?
Yes. The UK Biobank biomarker GWAS analyzed five population groups - White British, non-British White, African, South Asian, and East Asian participants - with a combined meta-analysis covering up to 355,891 individuals.