By definition

Allele:

- One of the variant forms of a gene at a particular locus, or location, on a chromosome.  Different alleles produce variation in inherited characteristics such as hair color or blood type.  In an individual, one form of the allele (the dominant one) may be expressed more than another form
(the recessive one). 

- An allele is one of a series of different forms of a gene.
The word is a short from of allelomorph ('other form'), which
was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes.  Alleles are now understood to be alternative DNA sequences at the same physical gene locus, which may or may not result in different phenotypic traits. 

More detail 1

From : Roberts Robert, McNally Elizabeth, "Chapter 9. Genetic Basis for Cardiovascular Disease " (Chapter). Fuster V, O’Rourke RA, Walsh RA, Poole-Wilson P, Eds. King SB, Roberts R, Nash IS, Prystowsky EN, Assoc. Eds.: Hurst's The Heart, 12e: http://www.accessmedicine.com/content.aspx?aID=3049742.

Chromosomal Loci, Genes, and Alleles

The precise position of each gene on the chromosome is identical from person to person and is referred to as the chromosomal locus. Chromosome loci are designated by giving the chromosome number (1–23, X, or Y) and whether it is on the long (q) or short arm (p) and the subband region. Subregions reflect the banding patterns of chromosomes based on Giemsa staining patterns. An example is the chromosomal locus for the gene that encodes for angiotensin-converting enzyme (ACE) is designated 17q23. Each pair of autosomal homologous chromosomes carry the same set of genes with one inherited from each parent. Despite their homology and the identical overall function of the genes, some genes have a slightly different DNA sequence from that of their corresponding genes on the other chromosome of the homologous pair, which may slightly or markedly alter the gene's function. For example, the gene encoding for ACE located at 17q23 is present at this locus on each homologous chromosome from both parents. However, the ACE gene is known to exist in the general population in three forms of alleles designated D, DI, and II. The particular allele accompanying the 17q23 locus depends on which alleles are inherited from the parents. If one inherits the D allele from the mother and the D allele from the father, they would be homozygous for the D allele; but if a parent had the D and the other the I allele, they would be heterozygous. Although both genes or alleles encode for ACE and convert angiotensinogen to angiotensin II, there is increased plasma enzyme activity associated with the D form, and studies suggest homozygosity for the D gene (DD), predisposes to cardiac hypertrophy. 6,7 Many genes exhibit multiple alleles.

More detail 2

From :Jameson J. L, Kopp Peter, "Chapter 62. Principles of Human Genetics" (Chapter). Fauci AS, Braunwald E, Kasper DL, Hauser SL, Longo DL, Jameson JL, Loscalzo J: Harrison's Principles of Internal Medicine, 17e: http://www.accessmedicine.com/content.aspx?aID=2879424.

Alleles, Genotypes, and Haplotypes

An observed trait is referred to as a phenotype ; the genetic information defining the phenotype is called the genotype . Alternative forms of a gene or a genetic marker are referred to as alleles. Alleles may be polymorphic variants of nucleic acids that have no apparent effect on gene expression or function. In other instances, these variants may have subtle effects on gene expression, thereby conferring the adaptive advantages associated with genetic diversity. On the other hand, allelic variants may reflect mutations in a gene that clearly alter its function. The common Glu6Val (E6V) sickle cell mutation in the -globin gene and the F508 deletion of phenylalanine (F) in the CFTR gene are examples of allelic variants of these genes that result in disease. Because each individual has two copies of each chromosome (one inherited from the mother and one inherited from the father), he or she can have only two alleles at a given locus. However, there can be many different alleles in the population. The normal or common allele is usually referred to as wild type. When alleles at a given locus are identical, the individual is homozygous . Inheriting identical copies of a mutant allele occurs in many autosomal recessive disorders, particularly in circumstances of consanguinity. If the alleles are different on the maternal and the paternal copy of the gene, the individual is heterozygous at this locus (Fig. 62-5). If two different mutant alleles are inherited at a given locus, the individual is said to be a compound heterozygote. Hemizygous is used to describe males with a mutation in an X chromosomal gene or a female with a loss of one X chromosomal locus.

Genotypes describe the specific alleles at a particular locus. For example, there are three common alleles (E2, E3, E4) of the apolipoprotein E (APOE) gene. The genotype of an individual can therefore be described as APOE3/4 or APOE4/4 or any other variant. These designations indicate which alleles are present on the two chromosomes in the APOE gene at locus 19q13.2. In other cases, the genotype might be assigned arbitrary numbers (e.g., 1/2) or letters (e.g., B/b) to distinguish different alleles.

A haplotype refers to a group of alleles that are closely linked together at a genomic locus (Fig. 62-8). Haplotypes are useful for tracking the transmission of genomic segments within families and for detecting evidence of genetic recombination, if the crossover event occurs between the alleles (Fig. 62-3). As an example, various alleles at the histocompatibility locus antigen (HLA) on chromosome 6p are used to establish haplotypes associated with certain disease states. For example, 21-hydroxylase deficiency, complement deficiency, and hemochromatosis are each associated with specific HLA haplotypes. It is now recognized that these genes lie in close vicinity to the HLA locus, which explains why HLA associations were identified even before the disease genes were cloned and localized. In other cases, specific HLA associations with diseases such as ankylosing spondylitis (HLA-B27) or type 1 diabetes mellitus (HLA-DR4) reflect the role of specific HLA allelic variants in susceptibility to these autoimmune diseases. The recent characterization of common SNP haplotypes in four populations from different parts of the world through the HapMap project is providing a novel tool for association studies designed to detect genes involved in the pathogenesis of complex disorders (Table 62-1). The presence or absence of certain haplotypes may also become relevant for the customized choice of medical therapies (pharmacogenomics) or for preventative strategies.