rs11206061 (SCP2): Height-Associated Genetic Variant
Key takeaways
- rs11206061 is one of 12,111 common variants tied to adult height in a study of approximately 5.4 million people.
- Together, these height variants explain roughly 40% of height differences in people of European ancestry.
- The ALT allele reduces SCP2 gene expression in heart tissue and boosts PODN expression in brain and arteries.
- Height prediction accuracy is much lower in non-European populations, reflecting gaps in current genetic reference data.
- The same variant also affects ECHDC2 expression in blood and spleen, suggesting biological reach beyond height.
Key takeaways
- rs11206061 is one of 12,111 common variants identified in a genome-wide association study of approximately 5.4 million people as significantly linked to adult height.
- Together, these height-associated variants explain roughly 40% of the differences in height between people of European ancestry.
- The ALT allele of rs11206061 reduces SCP2 (sterol carrier protein 2) expression in heart atrial appendage tissue and reduces CZIB-DT expression in thyroid tissue.
- The same allele increases PODN expression in brain, heart, and artery tissues, and increases ECHDC2 expression in blood, spleen, and aorta.
- Height prediction accuracy from these variants is substantially lower in non-European populations (roughly 10-20%), reflecting the European-heavy composition of the discovery sample.
What the research says rs11206061 was identified as one of 12,111 independent SNPs (single nucleotide polymorphisms, meaning single-letter changes at a fixed position in the DNA sequence) significantly associated with adult height in a genome-wide association study of approximately 5.4 million individuals drawn from 281 studies spanning European, East Asian, Hispanic, African, and South Asian ancestries. These variants collectively account for approximately 40% of the phenotypic variance (the total measurable variation in height between individuals) within populations of predominantly European ancestry, though prediction accuracy falls to roughly 10-20% in populations of other ancestries, a gap the study authors attribute to differences in linkage disequilibrium patterns (the tendency for nearby genetic variants to be inherited together) and allele frequency distributions rather than to differences in effect size. GTEx eQTL (expression quantitative trait locus, meaning a genetic variant that influences nearby gene expression levels) data show that this variant has tissue-specific expression effects on at least four nearby genes, including reduced expression of SCP2 in heart atrial appendage tissue GTEx Portal.
Reported associations
- Adult height: identified as one of 12,111 significantly associated common SNPs in a discovery GWAS of approximately 5.4 million participants across diverse ancestries; as a set, these 12,111 variants account for approximately 40% of height variance in European ancestry populations and approximately 10-20% in other ancestries.
Evidence quality The height association derives from a large GWAS encompassing approximately 5.4 million individuals across 281 studies and five major ancestry groups (roughly 76% European, 9% East Asian, 9% Hispanic, 6% African, and 1% South Asian ancestry). The authors characterize the map of height-associated SNPs as near-saturated for populations of European ancestry and note that effect sizes are broadly consistent across groups. Individual-SNP summary statistics (p-value, beta coefficient, or odds ratio) for rs11206061 specifically are not available in the provided study text, so variant-level effect size cannot be reported here. No conflicting findings are described for this variant. The GTEx eQTL data are drawn from GTEx v11 using 953 donors and meet a false discovery rate threshold below 5%, meaning fewer than 1 in 20 reported expression associations are expected to be false positives.
Tissue-specific expression effects
- SCP2: the ALT (alternative, non-reference) allele is associated with reduced expression in heart atrial appendage GTEx Portal
- PODN: the ALT allele is associated with increased expression in brain cerebellum, heart atrial appendage, and tibial artery GTEx Portal
- ECHDC2: the ALT allele is associated with increased expression in spleen, whole blood, and aortic artery GTEx Portal
- CZIB-DT: the ALT allele is associated with reduced expression in thyroid GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
Is rs11206061 linked to height?
Yes. rs11206061 was identified as one of 12,111 common genetic variants significantly associated with adult height in a genome-wide study of approximately 5.4 million people across diverse ancestries.
What gene is rs11206061 near?
rs11206061 is located near the SCP2 gene, which encodes sterol carrier protein 2. GTEx data show that the ALT allele is associated with reduced SCP2 expression specifically in heart atrial appendage tissue.
What does rs11206061 do to gene expression?
GTEx eQTL data show the ALT allele is associated with reduced SCP2 expression in heart tissue and reduced CZIB-DT expression in thyroid, while increasing PODN expression in brain, heart, and arteries, and increasing ECHDC2 expression in blood and spleen. These are expression-level findings and do not by themselves indicate disease risk.
How much of height does rs11206061 explain on its own?
An individual effect size for rs11206061 is not available in the provided study text. As part of the full set of 12,111 height-associated SNPs reported in the same study, the group collectively accounts for roughly 40% of height variance in European ancestry populations and 10-20% in other populations.
Why is height prediction less accurate in non-European populations?
Roughly 76% of participants in the discovery GWAS were of European ancestry. The study authors attribute lower prediction accuracy in other populations to differences in linkage disequilibrium patterns and allele frequencies, not to different biological effect sizes across ancestry groups.