rs11027948 (LUZP2): Educational Attainment Variant
Key takeaways
- rs11027948 was among 3,952 genome-wide significant variants for educational attainment in a study of approximately 3 million individuals
- The full polygenic score built from all such variants explains 12-16% of the variation in years of schooling completed
- The ALT allele reduces LUZP2 gene expression in brain substantia nigra and esophagus mucosa, based on GTEx tissue expression data
- No individual effect size for rs11027948 is specifically reported in available study texts; evidence comes from large-scale discovery data
Key takeaways
- rs11027948 was among 3,952 genome-wide significant variants for educational attainment in a study of approximately 3 million individuals
- The full polygenic score built from all such variants explains 12-16% of the variation in years of schooling completed
- The ALT allele reduces LUZP2 gene expression in brain substantia nigra and esophagus mucosa, based on GTEx tissue expression data
- No individual effect size for rs11027948 is specifically reported in available study texts; evidence comes from large-scale discovery data
What the research says A genome-wide association study (GWAS - a method of scanning hundreds of thousands of genetic markers across many people to find associations with traits) of educational attainment in approximately 3,037,499 individuals identified 3,952 approximately uncorrelated genome-wide-significant autosomal variants, with rs11027948 among them; the polygenic index (a single combined score derived from all significant variants together) derived from this analysis explains 12-16% of educational attainment variance across validation samples. Separately, expression quantitative trait locus (eQTL) data - which links genetic variants to changes in gene activity levels - from GTEx indicates the ALT allele of this variant is associated with reduced LUZP2 expression in esophagus mucosa (slope -0.25, p=1.3x10^-8) and brain substantia nigra (slope -0.19, p=1.8x10^-5) GTEx Portal. No available study provides a per-SNP effect size for rs11027948 individually, nor reports lifestyle or pharmacogenomic associations specific to this locus.
Reported associations
- Educational attainment: rs11027948 reached genome-wide significance in a meta-analysis of ~3,037,499 individuals for years of schooling completed; it is one of 3,952 independent loci, and a polygenic score built from all such loci explains 12-16% of variance in educational attainment
- LUZP2 expression in esophagus mucosa: the ALT allele is associated with reduced LUZP2 expression (slope -0.25, p=1.3x10^-8) GTEx Portal
- LUZP2 expression in brain substantia nigra: the ALT allele is associated with reduced LUZP2 expression (slope -0.19, p=1.8x10^-5) GTEx Portal
Evidence quality The educational attainment association is supported by a large discovery meta-analysis (N=3,037,499) spanning multiple cohorts, with a mean chi-squared statistic of 4.90 across included SNPs, consistent with a highly polygenic trait where most individual variants contribute small effects. This study expanded a prior cohort of roughly 1.1 million individuals to approximately 3 million by incorporating a substantially larger commercial genetics sample. Crucially, no per-SNP effect size or independent replication status for rs11027948 specifically is reported in the available study text; the evidence for this locus is therefore best characterised as large-scale discovery-stage. The eQTL associations come from GTEx v11 (953 donors, cis-window analysis, FDR<0.05), with the esophagus mucosa signal reaching p=1.3x10^-8 and the brain substantia nigra signal reaching p=1.8x10^-5; these represent an independent functional line of evidence distinct from the behavioral GWAS. No conflicting findings are present in the available literature.
Tissue-specific expression effects
- LUZP2: the ALT allele is associated with reduced expression in esophagus mucosa and brain substantia nigra; the effect is present across two anatomically distinct tissue types, suggesting a regulatory role for this genomic position GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs11027948 associated with?
rs11027948 reached genome-wide significance for educational attainment in a large study of approximately 3 million individuals. It is also linked to reduced expression of the LUZP2 gene in brain substantia nigra and esophagus mucosa, based on GTEx tissue data.
Is rs11027948 a major gene for intelligence or education?
No single variant, including rs11027948, is a major determinant of educational attainment. It is one of roughly 4,000 variants identified in a very large discovery study, and all of those variants combined explain only 12-16% of the variation in years of schooling.
What does LUZP2 expression in the brain mean for this variant?
GTEx data shows that carriers of the ALT allele tend to have lower LUZP2 expression in the brain's substantia nigra. This is a gene-expression effect, not a direct measure of brain function or behavior, and its downstream significance is not established in available literature.
What does it mean to carry the ALT allele of rs11027948?
Carriers of the ALT allele show reduced LUZP2 expression in esophagus mucosa and brain substantia nigra based on GTEx data. The specific directional effect of this variant on educational attainment is not described for this individual SNP in available study texts.
Where in the genome is rs11027948 located?
rs11027948 is annotated as being in the Y_RNA - LUZP2 genomic region. GTEx data confirms it has cis-regulatory effects on the LUZP2 gene in specific tissues, meaning it influences gene activity in nearby genomic territory.