User:Amorack/sandbox

Applications
Variations in the sequence of DNA such as SNPs can affect the progression of diseases and individual responses to pathogens, chemicals, drugs, vaccines, and other agents. Consequently, the study of SNPs is critical for personalized medicine. More generally, applications of the study of SNPs include biomedical research, forensics, pharmacogenetics, and disease causation. Genetic association studies can determine whether a genetic variant is associated with a particular disease or trait. Linkage disequilibrium (LD), a term used in population genetics, indicates non-random association of alleles at two or more loci, not necessarily on the same chromosome. It refers to the phenomenon that SNPs or other DNA sequences that are close together in the genome tend to be inherited together. LD can be affected by two parameters (among other factors, such as population stratification): 1) The distance between the SNPs, where a larger distance lowers the LD, and 2) Recombination rate, with a lower recombination rate leading to a higher LD. A "tag SNP" is a representative SNP in a region of the genome with high LD, and these tag SNPs are useful in whole-genome SNP association studies which examine hundreds of thousands of SNPs across the entire genome. In haplotype mapping, sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs. In genetic epidemiology, SNPs are used to estimate transmission clusters.

Examples

 * rs6311 and rs6313 are SNPs in the Serotonin 5-HT2A receptor gene on human chromosome 13.
 * The SNP − 3279C/A (rs3761548) is amongst the SNPs locating in the promoter region of the Foxp3 gene, might be involved in cancer progression.
 * A SNP in the F5 gene causes Factor V Leiden thrombophilia. Fvl pcr.jpg
 * rs3091244 is an example of a triallelic SNP in the CRP gene on human chromosome 1.
 * TAS2R38 codes for PTC tasting ability, and contains 6 annotated SNPs.
 * rs148649884 and rs138055828 in the FCN1 gene encoding M-ficolin crippled the ligand-binding capability of the recombinant M-ficolin.
 * An intronic SNP in DNA mismatch repair gene PMS2 (rs1059060, Ser775Asn) is associated with increased sperm DNA damage and risk of male infertility.