rs1204836 (NT5DC1): Adult Height Variant
Key takeaways
- rs1204836 is one of 12,111 SNPs linked to adult height in the largest height GWAS to date, a study of up to 5.4 million people across diverse ancestries
- The variant lies near NT5DC1, a gene in one of roughly 7,209 height-associated genomic segments identified across the genome
- GTEx data shows this locus associates with increased expression of CALHM6 in brain frontal cortex, putamen, fibroblasts, pituitary, lung, and whole blood
- It also associates with increased TSPYL4 expression in esophageal tissue and fibroblasts
- Height predictions based on common SNPs identified mainly in European ancestry cohorts explain about 40% of height variance in that group but only 10-20% in other ancestry groups
Key takeaways
- rs1204836 is one of 12,111 SNPs linked to adult height in the largest height GWAS to date, a study of up to 5.4 million people across diverse ancestries
- The variant lies near NT5DC1, a gene residing in one of roughly 7,209 height-associated genomic segments identified across the genome
- GTEx data shows this locus associates with increased expression of CALHM6 in brain frontal cortex, putamen, fibroblasts, pituitary, lung, and whole blood
- It also associates with increased TSPYL4 expression in esophageal tissue and fibroblasts
- Height predictions based on common SNPs identified mainly in European ancestry cohorts explain about 40% of height variance in that group but only 10-20% in other ancestry groups
What the research says A genome-wide association study of up to 5,380,080 individuals from 281 studies identified 12,111 independent SNPs significantly associated with adult height, with rs1204836 near NT5DC1 among the mapped loci. These height-associated SNPs cluster within roughly 7,209 non-overlapping genomic segments covering about 21% of the genome and collectively account for nearly all common SNP-based heritability for the trait. The study enrolled participants of predominantly European (75.8%), East Asian (8.8%), Hispanic (8.5%), African (5.5%), and South Asian (1.4%) ancestries. GTEx v11 data (953 donors, FDR < 0.05) links this locus to increased expression of CALHM6 in six tissue types and increased TSPYL4 expression in two tissue types GTEx Portal.
Reported associations
- Adult height: rs1204836 was identified as one of 12,111 independent genome-wide-significant SNPs for height in a study of up to 5,380,080 individuals; the full set of these SNPs explains about 40% of height variance in European ancestry populations and approximately 10-20% in other ancestry groups
- CALHM6 expression - brain: the alternate allele of this locus associates with increased CALHM6 expression in frontal cortex (BA9) and putamen (basal ganglia), with the frontal cortex showing the largest effect size by slope among all tested tissues GTEx Portal
- CALHM6 expression - peripheral tissues: the alternate allele associates with increased CALHM6 expression in cultured fibroblasts, pituitary, lung, and whole blood; fibroblasts show the strongest statistical signal across all tissue associations for this gene GTEx Portal
- TSPYL4 expression: the alternate allele associates with increased TSPYL4 expression in esophageal mucosa and cultured fibroblasts, with the fibroblast signal showing a stronger statistical association than the esophageal one GTEx Portal
Evidence quality The height association derives from one of the largest genetic studies ever conducted, with up to 5,380,080 participants drawn from 281 studies and genome-wide significance thresholds applied across 12,111 independent loci. The participant pool was predominantly European ancestry (75.8%), which limits direct extrapolation of individual SNP findings to other groups. No PMID was included in the study metadata provided, so inline study citations for height claims are omitted per source policy. The GTEx v11 eQTL associations are based on 953 donors in a cis-window analysis at FDR < 0.05; CALHM6 eQTL p-values across tissues range from 8.0e-5 (brain frontal cortex) to 1.7e-9 (cultured fibroblasts), and TSPYL4 eQTL p-values range from 3.6e-7 (esophageal mucosa) to 2.4e-9 (cultured fibroblasts). These figures reflect statistical links between genotype and transcript abundance in population-level data rather than experimental functional validation. All observed eQTL effects for this locus are in the same direction (increased expression), with no conflicting signals across the provided tissue data GTEx Portal.
Tissue-specific expression effects
- CALHM6: the alternate allele associates with increased expression in brain frontal cortex (BA9), brain putamen (basal ganglia), cultured fibroblasts, pituitary, lung, and whole blood; the frontal cortex shows the largest expression change by effect size, while fibroblasts show the strongest statistical signal across all tissues GTEx Portal
- TSPYL4: the alternate allele associates with increased expression in esophageal mucosa and cultured fibroblasts GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs1204836 and what gene is it near?
rs1204836 is a common single-nucleotide polymorphism (a single-letter DNA variant) located near NT5DC1. It was identified in one of the largest genetic studies of human height to date, involving over 5.4 million participants across diverse ancestries.
Is rs1204836 linked to height?
Yes. rs1204836 is among 12,111 independent SNPs identified as significantly associated with adult human height in a genome-wide association study of up to 5,380,080 individuals spanning five major ancestry groups.
What tissues does rs1204836 affect gene expression in?
GTEx v11 data links the alternate allele of rs1204836 to increased CALHM6 expression in brain frontal cortex, putamen, fibroblasts, pituitary, lung, and whole blood, and to increased TSPYL4 expression in esophageal mucosa and fibroblasts.
Does this height SNP predict height equally in all ancestry groups?
No. The set of height-associated SNPs, including rs1204836, was identified mainly in European ancestry populations and explains about 40% of height variation in that group but only roughly 10-20% in other ancestry groups, due to differences in linkage disequilibrium and allele frequencies across populations.
What does CALHM6 do?
The provided studies identify CALHM6 as a gene whose expression is increased by the alternate allele of rs1204836 across multiple tissues including brain regions, fibroblasts, lung, and blood. The provided research does not detail its specific biological function beyond these expression associations.