Expressive

rs1129671 (FLRT2): Educational Attainment Variant

Key takeaways

  • rs1129671 in the FLRT2 gene region reached genome-wide significance for educational attainment in a study of about 3 million people.
  • Polygenic scores built from this and similar variants explain 12-16% of variation in years of schooling completed.
  • Direct genetic effects account for roughly half the polygenic association with educational attainment; the rest may reflect family or social factors.
  • The alternate allele is linked to reduced FLRT2 expression in cervical spinal cord tissue and increased expression in cultured fibroblasts, based on GTEx data.

Key takeaways

  • rs1129671, located in the FLRT2 gene region, was identified as one of 3,952 genome-wide significant variants associated with educational attainment in a study of about 3 million people.
  • Polygenic scores built from this and similar variants explain 12-16% of variation in years of schooling completed.
  • Direct genetic effects account for roughly half the total polygenic association with educational attainment; the remainder may reflect shared family or social environments.
  • The alternate allele is linked to reduced FLRT2 expression in cervical spinal cord tissue and increased FLRT2 expression in cultured fibroblasts, based on GTEx reference data.

What the research says A genome-wide association study (GWAS) of educational attainment (EA, meaning years of schooling completed) in approximately 3,037,499 individuals identified 3,952 approximately uncorrelated, genome-wide-significant single-nucleotide polymorphisms (SNPs, or single-letter DNA variants); rs1129671 in the FLRT2 gene region was among these, with the derived polygenic index explaining 12-16% of EA variance in independent samples, a roughly 20% improvement over the prior generation of the study. Analyses accounting for parental genetics found that direct genetic effects explain approximately half the total polygenic association with EA, suggesting the remainder reflects indirect or environmental factors. Separately, GTEx eQTL reference data (953 donors) show the alternate allele is associated with reduced FLRT2 expression in cervical spinal cord tissue and increased expression in cultured fibroblasts GTEx Portal.

Reported associations

  • Educational attainment (years of schooling): rs1129671 was identified as genome-wide significant in a GWAS of approximately 3,037,499 individuals; polygenic indices incorporating this and similar variants explain 12-16% of variance in years of schooling in independent validation samples.

Evidence quality The association with educational attainment is drawn from a single large-scale GWAS meta-analysis (N approximately 3,037,499), the largest of its kind at the time of publication, with a mean chi-squared statistic of 4.90 across all included SNPs with minor allele frequency above 1%. Polygenic prediction was validated in independent samples including the Health and Retirement Study and the National Longitudinal Study of Adolescent to Adult Health, where incremental R2 estimates were computed after controlling for year of birth, sex, and the first ten principal components of genomic relatedness. No published replication study specifically for rs1129671 is included in the provided literature, and no conflicting associations are reported. The GTEx eQTL associations are statistically robust (p = 1.5e-14 in cervical spinal cord; p = 4.4e-7 in cultured fibroblasts) but describe gene-regulation patterns in reference tissues, not clinical outcomes GTEx Portal.

Tissue-specific expression effects

  • FLRT2: The alternate allele is associated with reduced expression in cervical spinal cord tissue and increased expression in cultured fibroblasts GTEx Portal.

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs1129671 associated with?

rs1129671 in the FLRT2 gene region has been identified as genome-wide significant for educational attainment, specifically years of schooling completed, in a genome-wide association study of approximately 3 million individuals.

What is the FLRT2 gene?

FLRT2 is the gene in whose region rs1129671 is located. GTEx reference data show that this variant is associated with altered FLRT2 gene expression in cervical spinal cord tissue and in cultured fibroblasts, though the provided research does not detail the specific biological function of the gene.

How much does rs1129671 influence educational attainment?

No single-variant effect size for rs1129671 alone is reported in the provided study. Polygenic scores combining this and thousands of similar variants explain 12-16% of variance in years of schooling in independent samples, a roughly 20% improvement over earlier studies.

Is rs1129671 linked to intelligence or cognitive ability?

The provided study reports an association with educational attainment as measured by years of schooling. The same polygenic index also adds predictive power for cognitive phenotypes and ten diseases, but specific cognitive associations for rs1129671 alone are not detailed in the provided literature.

Is the effect of rs1129671 on education purely genetic?

Not entirely. Analyses in the provided study found that direct genetic effects explain roughly half the polygenic score's association with educational attainment, suggesting the remainder may reflect indirect family-level or social environmental factors.