Sometimes, only a subset of the cases in a group will be explained by variants in the same gene, thus diluting the strength of phenotypic similarity of the entire group.
Furthermore, if much of the genetic variance of interest is explained by variants in or near transcribed genes, then these markers may be more efficient than randomly distributed markers.
Alternatively, rs11568506 might be in high LD with another, untested SNP closer to IL13 so that the 'independent' effect could be explained by another variant within or near IL13.
We used a variance component analysis to determine how much variance can be explained by the variants in each class, over and above the same number of randomly chosen intergenic variants.
On the other hand, a significant amount of phenotypic variation can be explained by common variants, as long as genome-wide SNPs are jointly analyzed (Yang et al. 2010; Zhou et al. 2013).
There is sustained debate between those who believe the missing disease contributions will be explained by rare variants with a large effect or common variants with small effects.
The so-called 'missing heritability' may be explained by common variants with very small effects and/or by rarer variants with larger effects, neither of which can be identified by current genome-wide association studies.
To estimate how much of the variance for ASD can be explained by common variants, the allele score derived from the Stage 1 data (21) was used to predict case status in the Stage 2 data and calculate the VM.
Indeed, for Crohn's disease, it has been estimated that 22% of the differences in individual disease risk seen in the population (variance in disease liability) can be explained by common variants tagged on microarrays [63] – more than double that explained by known risk loci [64].
In general, only 1.5%50%% of heritability of common complex diseases and traits can be explained by common variants [16].
