rs1156541 (LINC00907): Educational Attainment SNP

Key takeaways

• rs1156541 is one of 3,952 variants genome-wide linked to educational attainment in a study of about 3 million people.
• All these variants together explain 12-16% of the variation in years of schooling completed.
• Only about half of the genetic association is a direct effect; the rest reflects shared family environment and other indirect pathways.
• No non-additive (dominance) genetic effects were found at any educational attainment locus.
• No lifestyle considerations are currently on file for this specific variant.

What the research says rs1156541 falls within the LINC00907 locus and was identified among 3,952 approximately uncorrelated genome-wide-significant single-nucleotide polymorphisms (SNPs, single letters in the DNA code that vary between people) in a meta-analysis of educational attainment (EA, the number of years of schooling completed) encompassing approximately 3 million participants. The polygenic index (PGI, a score that sums many small genetic signals to estimate a trait) constructed from these findings explains 12-16% of EA variance across validation samples, an increase of roughly 20% over the prior study in 1.1 million individuals. Direct effects of the PGI, estimated by controlling for parental genotypes to separate inherited biology from shared family environment, explain approximately half the PGI's overall predictive magnitude for EA and other phenotypes.

Reported associations

• Educational attainment (years of schooling): rs1156541 is one of 3,952 SNPs reaching genome-wide significance for EA in approximately 3 million individuals; the combined PGI for all loci explains 12-16% of EA variance, up from 10-13% in the previous generation of this research.
• Disease risk prediction: The EA polygenic index, which includes this locus among thousands of others, adds predictive power for ten diseases examined beyond what years of schooling alone contributes; individual variant contributions to disease risk are not reported separately.
• Additive genetic architecture: A dominance GWAS (testing non-additive, or interaction-type, genetic effects at each SNP) in approximately 2.57 million individuals found no genome-wide-significant results, indicating that EA loci including this one behave consistently with a simple additive model.
• X chromosome (separate analysis): A parallel X-chromosome GWAS in approximately 2.71 million individuals identified 57 genome-wide-significant loci; rs1156541 is an autosomal (non-sex-chromosome) variant and is not part of this set.

Evidence quality The association derives from one of the largest GWAS meta-analyses conducted to date, covering approximately 3 million individuals and yielding 3,952 independent genome-wide-significant loci. Genome-wide significance thresholds were applied to control false-positive rates. The PGI R2 figures of 12-16% come from external validation in the Health and Retirement Study and the National Longitudinal Study of Adolescent to Adult Health, rather than in the discovery sample, which reduces the risk of overfitting. The dominance analysis in approximately 2.57 million individuals detected no significant non-additive effects, and the authors state they can rule out with high confidence any common SNP whose dominance contribution to EA variance is more than negligible. No effect size specific to rs1156541 alone is reported in the provided study text; the 12-16% variance figure applies to the full PGI of 3,952 loci combined, not to any single variant. The study did not separately replicate individual SNPs outside the meta-analytic framework.

Lifestyle considerations No lifestyle considerations on file for this variant.