Databases
As there are for genes, bioinformatics databases exist for SNPs. dbSNP is a SNP database from the National Center for Biotechnology Information (NCBI). SNPedia is a wiki-style database supporting personal genome annotation, interpretation and analysis. The OMIM database describes the association between polymorphisms and diseases (e.g., gives diseases in text form), the Human Gene Mutation Database provides gene mutations causing or associated with human inherited diseases and functional SNPs, and GWAS Central allows users to visually interrogate the actual summary-level association data in one or more genome-wide association studies. The International SNP Map working group mapped the sequence flanking each SNP by alignment to the genomic sequence of large-insert clones in Genebank. These Alignments were converted to chromosomal coordinates that is show in Table 1 Another database is the International HapMap Project, where researches are identifying Tag SNP to be able to determine the collection of haplotypes present in each subject.
| Chromosome | Length(bp) | All SNPs | TSC SNPs | ||
|---|---|---|---|---|---|
| SNPs | kb per SNP | SNPs | kb per SNP | ||
| 1 | 214,066,000 | 129,931 | 1.65 | 75,166 | 2.85 |
| 2 | 222,889,000 | 103,664 | 2.15 | 76,985 | 2.90 |
| 3 | 186,938,000 | 93,140 | 2.01 | 63,669 | 2.94 |
| 4 | 169,035,000 | 84,426 | 2.00 | 65,719 | 2.57 |
| 5 | 170,954,000 | 117,882 | 1.45 | 63,545 | 2.69 |
| 6 | 165,022,000 | 96,317 | 1.71 | 53,797 | 3.07 |
| 7 | 149,414,000 | 71,752 | 2.08 | 42,327 | 3.53 |
| 8 | 125,148,000 | 57,834 | 2.16 | 42,653 | 2.93 |
| 9 | 107,440,000 | 62,013 | 1.73 | 43,020 | 2.50 |
| 10 | 127,894,000 | 61,298 | 2.09 | 42,466 | 3.01 |
| 11 | 129,193,000 | 84,663 | 1.53 | 47,621 | 2.71 |
| 12 | 125,198,000 | 59,245 | 2.11 | 38,136 | 3.28 |
| 13 | 93,711,000 | 53,093 | 1.77 | 35,745 | 2.62 |
| 14 | 89,344,000 | 44,112 | 2.03 | 29,746 | 3.00 |
| 15 | 73,467,000 | 37,814 | 1.94 | 26,524 | 2.77 |
| 16 | 74,037,000 | 38,735 | 1.91 | 23,328 | 3.17 |
| 17 | 73,367,000 | 34,621 | 2.12 | 19,396 | 3.78 |
| 18 | 73,078,000 | 45,135 | 1.62 | 27,028 | 2.70 |
| 19 | 56,044,000 | 25,676 | 2.18 | 11,185 | 5.01 |
| 20 | 63,317,000 | 29,478 | 2.15 | 17,051 | 3.71 |
| 21 | 33,824,000 | 20,916 | 1.62 | 9,103 | 3.72 |
| 22 | 33,786,000 | 28,410 | 1.19 | 11,056 | 3.06 |
| X | 131,245,000 | 34,842 | 3.77 | 20,400 | 6.43 |
| Y | 21,753,000 | 4,193 | 5.19 | 1,784 | 12.19 |
| RefSeq | 15,696,674 | 14,534 | 1.08 | ||
| Totals | 2,710,164,000 | 1,419,190 | 1.91 | 887,450 | 3.05 |
Read more about this topic: Single Nucleotide Polymorphism