rs11113204 (CRY1/SETP7): Height GWAS Variant
Key takeaways
- rs11113204 is one of 12,111 SNPs linked to adult height in a genome-wide study of 5.4 million people.
- The alternate allele increases CRY1 expression in testis and skeletal muscle.
- This variant also alters expression of three other nearby genes in skin and esophageal tissue.
- Height prediction from this full SNP set reaches 40-45% variance explained in European-ancestry populations, but is lower in other ancestry groups.
Key takeaways
- rs11113204 is one of 12,111 SNPs linked to adult height in a genome-wide study of 5.4 million people.
- The alternate allele at this position increases CRY1 expression in testis and skeletal muscle.
- This variant also alters expression of three other nearby genes (ENSG00000306026, ABTB3, MTERF2) in skin and esophageal tissue.
- Height prediction from this full SNP set reaches 40-45% variance explained in European-ancestry populations, but is lower in other ancestry groups.
What the research says rs11113204, near the CRY1 and SETP7 genes, was identified as one of 12,111 SNPs (single-nucleotide polymorphisms, common single-letter differences in the genetic code) significantly associated with adult height in a meta-analysis (a pooled combined analysis) of approximately 5.4 million individuals from 281 studies spanning five major ancestry groups. The full set of identified SNPs clusters within 7,209 non-overlapping genomic segments covering roughly 21% of the human genome, and collectively accounts for about 40-45% of the phenotypic variance (the measurable variation across a population) in height within European-ancestry samples, dropping to 10-24% in non-European ancestry populations. GTEx eQTL (expression quantitative trait locus, meaning gene-activity associations tied to a specific genetic position) data indicates that the alternate allele at this locus is associated with increased CRY1 expression in testis and skeletal muscle, and with altered expression of three additional nearby genes across skin and esophageal tissue GTEx Portal.
Reported associations
- Adult height: rs11113204 is among 12,111 independently significant SNPs associated with adult height in a GWAS meta-analysis of approximately 5.4 million individuals from diverse ancestry groups (Nature, 2022). No per-SNP beta coefficient or odds ratio for this specific variant appears in the available study text.
Evidence quality The height association derives from a single large-scale meta-analysis of approximately 5.4 million individuals from 281 studies, making it one of the largest genetic association studies conducted for any human phenotype. The 12,111 identified SNPs are spread across 7,209 genomic segments spanning roughly 21% of the genome. The full SNP set explains about 40% of height variance in European-ancestry populations (rising to 45% when all HapMap 3 panel SNPs are included), but only 10-24% in non-European ancestry groups, a difference the study attributes to linkage disequilibrium (the tendency of nearby genetic variants to be co-inherited) and allele frequency variation across ancestry groups. No specific p-value or effect size for rs11113204 appears in the available study text, and no independent replication study for this particular variant is described in the provided materials. The GTEx eQTL findings are drawn from a separate dataset of 953 donors and represent mechanistic evidence about gene expression, not direct outcome evidence for height or other traits.
Tissue-specific expression effects
- CRY1: Increased expression in testis and skeletal muscle is associated with the alternate allele GTEx Portal.
- ENSG00000306026: Increased expression in non-sun-exposed suprapubic skin, sun-exposed lower leg skin, and esophageal mucosa is associated with the alternate allele GTEx Portal.
- ABTB3: Increased expression in sun-exposed lower leg skin is associated with the alternate allele GTEx Portal.
- MTERF2: Reduced expression in sun-exposed lower leg skin is associated with the alternate allele GTEx Portal.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs11113204?
rs11113204 is a common genetic variant located near the CRY1 and SETP7 genes. It was identified as one of 12,111 SNPs significantly associated with adult height in one of the largest genome-wide association studies ever conducted, covering approximately 5.4 million people.
Is rs11113204 linked to height?
Yes. A genome-wide association study of approximately 5.4 million individuals identified rs11113204 as one of 12,111 SNPs significantly associated with adult height. No specific effect size for this individual variant was reported in the available study text.
What does rs11113204 do to gene expression?
GTEx data shows the alternate allele at rs11113204 is associated with increased CRY1 expression in testis and skeletal muscle, increased expression of ENSG00000306026 and ABTB3 in skin, and decreased MTERF2 expression in skin.
How reliable is the height association for rs11113204?
The association comes from a very large meta-analysis of 5.4 million people from 281 studies, providing strong statistical power overall. However, no specific p-value or per-SNP effect size was reported for rs11113204 in the available study text, so the individual variant-level evidence strength cannot be directly assessed from the provided materials.
Why is height prediction accuracy lower in non-European populations?
The study found that the 12,111 height SNPs explain 40-45% of height variance in European-ancestry populations but only 10-24% in other groups. The researchers attribute this gap to differences in linkage disequilibrium and allele frequency patterns across ancestry groups.