What are variants, alleles and haplotypes?

What are variants?

In the field of genetic variation, the term variant is used to refer to a specific region of the genome which differs between two genomes.

What are alleles?

Different versions of the same variant are called alleles. For example, a SNP may have two alternative bases, or alleles, C and T4.

When working with genome scale data the term reference allele refers to the base that is found in the reference genome. Since the reference is just somebody’s genome, it is not always the major allele. In contrast, the alternative allele refers to any base, other than the reference, that is found at that locus. The alternative allele is not necessarily the minor allele and it may, or may not, be linked to a phenotype. There can be more than one alternative allele per variant.

What is linkage disequilibrium?

In the genome, alleles at variants close together on the same chromosome tend to occur together more often than is expected by chance. These blocks of alleles are called haplotypes. Linkage disequilibrium (LD) is a measure of how often two alleles or specific sequences are inherited together, with alleles that are always co-inherited said to be in linkage disequilibrium.