Related Experiment Video
Updated: Jun 12, 2026
10:17
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Common SNPs explain a large proportion of the heritability for human height
Jian Yang1, Beben Benyamin, Brian P McEvoy
1Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
Nature Genetics
|June 22, 2010
Summary
Most human height heritability is not missing but undetected. By analyzing all single nucleotide polymorphisms (SNPs) together, researchers found 45% of genetic variance, revealing that individual SNP effects are too small for standard significance tests.
Area of Science:
- Human Genetics
- Complex Traits
- Statistical Genomics
Background:
- Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) associated with complex traits.
- SNPs identified by GWASs explain only a small portion of the genetic variation for complex human traits, leading to the 'missing heritability' problem.
Purpose of the Study:
- To estimate the proportion of genetic variance for human height explained by a large set of genotyped SNPs.
- To investigate the reasons for the 'missing heritability' in complex traits.
Main Methods:
- Linear model analysis was used to estimate the variance explained by 294,831 SNPs in 3,925 unrelated individuals.
- Simulation studies based on observed genotype data were performed to validate the estimation method.
Main Results:
- Considering all SNPs simultaneously, 45% of the variance in human height could be explained.
- The majority of heritability for complex traits is not missing but has been previously undetected due to small individual SNP effects.
Conclusions:
- The 'missing heritability' is largely due to the cumulative effect of many SNPs with small individual effects that do not reach statistical significance.
- Incomplete linkage disequilibrium and lower minor allele frequencies of causal variants contribute to the underestimation of heritability by traditional GWAS.
Related Concept Videos
01:18Polygenic Traits
When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
01:18Polygenic Traits
When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
01:06Heritability
Heritability is a statistical concept that measures the degree to which genetic differences among individuals contribute to trait variations within a population. It is a fundamental idea in genetics, often prone to misinterpretation. Heritability is expressed as a percentage, reflecting the proportion of variation in a specific trait across a population that can be linked to genetic differences. However, it's important to understand that heritability does not determine how "genetic" a trait is,...
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
01:10Nature and Nurture
Many human characteristics, like height, are shaped by both nature—in other words, by our genes—and by nurture, or our environment. For example, chronic stress during childhood inhibits the production of growth hormones and consequently reduces bone growth and height. Scientists estimate that 70-90% of variation in height is due to genetic differences among individuals, and 10-30% of variation in height is due to differences in the environments that individuals experience, such as differences...