dinucleotide repeat (ac)n) are termed microsatellite sequences. among the microsatellite sequences, trinucleotide repeats are of particular importance, as sometimes occur within coding regions of genes for proteins and may lead to genetic disorders. for example, huntington's disease results from an expansion of the trinucleotide repeat (cag)n within the huntingtin gene on human chromosome 4. telomeres (the ends of linear chromosomes) end with a microsatellite hexanucleotide repeat of the sequence (ttaggg)n. tandem repeats of longer sequences (arrays of repeated sequences 10–60 nucleotides long) are termed minisatellites. mobile genetic elements (transposons) and their relics transposable genetic elements, dna sequences that can replicate and insert copies of themselves at other locations within a host genome, are an abundant component in the human genome. the most abundant transposon lineage, alu, has about 50,000 active copies, and can be inserted into intragenic and intergenic regions. one other lineage, line-1, has about 100 active copies per genome (the number varies between people). together with non-functional relics of old transposons, they account for over half of total human dna. sometimes called "jumping genes", transposons have played a major role in sculpting the human genome. some of these sequences represent endogenous retroviruses, dna copies of viral sequences that have become permanently integrated into the genome and are now passed on to succeeding generations. mobile elements within the human genome can be classified into ltr retrotransposons (8.3% of total genome), sines (13.1% of total genome) including alu elements, lines (20.4% of total genome), svas (sine-vntr-alu) and class ii dna transposons (2.9% of total genome). genomic variation in humans human reference genome with the exception of identical twins, all humans show significant variation in genomic dna sequences. the human reference genome (hrg) is used as a standard sequence reference. there are several important points concerning the human reference genome: the hrg is a haploid sequence. each chromosome is represented once. the hrg is a composite sequence, and does not correspond to any actual human individual. the hrg is periodically updated to correct errors, ambiguities, and unknown "gaps". the hrg in no way represents an "ideal" or "perfect" human individual. it is simply a standardized representation or model that is used for comparative purposes. the genome reference consortium is responsible for updating the hrg. version 38 was released in december 2013. measuring human genetic variation most studies of human genetic variation have focused on single-nucleotide polymorphisms (snps), which are substitutions in individual bases along a chromosome. most analyses estimate that snps occur 1 in 1000 base pairs, on average, in the euchromatic human genome, although they do not occur at a uniform density. thus follows the popular statement that "we are all, regardless of race, genetically 99.9% the same", although this would be somewhat qualified by most geneticists. for example, a much larger fraction of the genome is now thought to be involved in copy number variation. a large-scale collaborative effort to catalog snp variations in the human genome is being undertaken by the international hapmap project. the genomic loci and length of certain types of small repetitive sequences are highly variable from person to person, which is the basis of dna fingerprinting and dna paternity testing technologies. the heterochromatic portions of the human genome, which total several hundred million base pairs, are also thought to be quite variable within the human population (they are so repetitive and so long that they cannot be accurately sequenced with current technology). these regions contain few genes, and it is unclear whether any significant phenotypic effect results from typical variation in repeats or heterochromatin. most gross genomic mutations in gamete germ cells probably result in inviable embryos; however, a number of human diseases are related to large-scale genomic abnormalities. down syndrome, turner syndrome, and a number of other diseases result from nondisjunction of entire chromosomes. cancer cells frequently have aneuploidy of chromosomes and chromosome arms, although a cause and effect relationship between aneuploidy and cancer has not been established. mapping human genomic variation whereas a genome sequence lists the order of every dna base in a genome, a genome map identifies the landmarks. a genome map is less detailed than a genome sequence and aids in navigating around the genome. an example of a variation map is the hapmap being developed by the international hapmap project. the hapmap is a haplotype map of the human genome, "which will describe the common patterns of human dna sequence variation." it catalogs the patterns of small-scale variations in the genome that involve single dna letters, or bases. researchers published the first sequence-based map of large-scale structural variation across the human genome in the journal nature in may 2008. large-scale structural variations are differences in the genome among people that range from a few thousand to a few million dna bases; some are gains or losses of stretches of genome sequence and others appear as re-arrangements of stretches of sequence. these variations include differences in the number of copies individuals have of a particular gene, deletions, translocations and inversions. structural variation structural variation refers to genetic variants that affect larger segments of the human genome, as opposed to point mutations. often, structural variants (svs) are defined as variants of 50 base pairs (bp) or greater, such as deletions, duplications, insertions, inversions and other rearrangements. about 90% of structural variants are noncoding deletions but most individuals have more than a thousand such deletions; the size of deletions ranges from dozens of base pairs to tens of thousands of bp. on average, individuals carry ~3 rare structural variants that alter coding regions, e.g. delete exons. about 2% of individuals carry ultra-rare megabase-scale structural variants, especially rearrangements. that is, millions of base pairs may be inverted within a chromosome; ultra-rare means that they are only found in individuals or their family members and thus have arisen very recently. snp frequency across the human genome single-nucleotide polymorphisms (snps) do not occur homogeneously across the human genome. in fact, there is enormous diversity in snp frequency between genes, reflecting different selective pressures on each gene as well as different mutation and recombination rates across the genome. however, studies on snps are biased towards coding regions, the data generated from them are unlikely to reflect the overall distribution of snps throughout the genome. therefore, the snp consortium protocol was designed to identify snps with no bias towards coding regions and the consortium's 100,000 snps generally reflect sequence diversity across the human chromosomes. the snp consortium aims to expand the number of snps identified across the genome to 300 000 by the end of the first quarter of 2001. tsc snp distribution along the long arm of chromosome 22 (from https://web.archive.org/web/20130903043223/http://snp.cshl.org/ ). each column represents a 1 mb interval; the approximate cytogenetic position is given on the x-axis. clear peaks and troughs of snp density can be seen, possibly reflecting different rates of mutation, recombination and selection.changes in non-coding sequence and synonymous changes in coding sequence are generally more common than non-synonymous changes, reflecting greater selective pressure reducing diversity at positions dictating amino acid identity. transitional changes are more common than transversions, with cpg dinucleotides showing the highest mutation rate, presumably due to deamination. personal genomes