SNP Websites

Database	Institution	Notes	Approximate size (human data only)	Submit to dbSNP
dbSNP	NCBI	Official repository of public SNP data	10 million unique SNPs	NA
HapMap project	International consortium	Basic SNP information and allele frequencies in dbSNP Must register to see genotypes (anyone can register)	3 million SNPs submitted to dbSNP. 500,000 SNPs genotyped in 90 individuals	Yes (see notes)
JSNP	University of Tokyo	SNP discovery and validation in Japanese population Part of HapMap	200,000 SNPs 85,000 with frequencies	Yes
Nickerson Group	University of Washington and many collaborators	MDECODE. Study of common genetic variation in the population at large PARC. SNP discovery and validation in genes involved in cardiovascular disease EST cSNPs. cSNP discovery by EST sequence comparison TCR beta. SNP discovery and validation is T cell receptor beta locus	MDECODE. 13 genes PARC. 24 genes EST. 165 genes, 201 cSNPs TCR beta. 279 SNPs	Some
Seattle SNPs PGA	University of Washington and the Fred Hutchinson Cancer Research Center	SNP discovery and validation in genes involved in inflammatory responses	163 genes finished 26 in progress 136 proposed	Yes
Innate Immunity PGA	University of Arizona, Brigham and Women’s Hospital, Boston Children’s Hospital	SNP discovery and validation in genes of innate immunity pathway, followed by disease association studies	80 genes 6500 SNPs	Yes
Southwestern PGA	University of Texas Southwestern	SNP discovery and validation that may cause heart disease	355 genes	Yes
CardioGenomics SNPs PGA	Harvard Medical School and Whitehead Institute	SNP discovery and validation in genes involved in cardiac disease	130 genes 3,700 SNPs	Yes
NIEHS Environmental Genome Project	University of Washington	SNP discovery and validation in genes involved in DNA repair and cell cycle pathways	218 genes finished 47 in progress 151 proposed	Yes
Environmental Genome SNP (egSNP)	NIEHS	SNP discovery and validation in selected environmental response genes. listed	31 genes	Yes
GeneSNPs	University of Utah	Repository for Environmental Genome Project. Nice browser with links to PDB.	584 genes	Yes
CGAP Genetic Annotation Initiative (GAI) and SNP500	National Cancer Institute	Data mining and resequencing of cancer related genes. GAI’s validated SNPs are in dbSNP; candidates are not. I don’t know about SNP500.	GAI has validated SNPs in 4000 genes and candidates in 11,500. SNP500 has “analyzed” SNPs in 424 genes and “pending” SNPs in 275	See notes
Human Gene Mutation Database (HGMD)	University of Wales	Curated data on mutations of all sorts associated with disease Data cannot be downloaded	1,500 genes 40,000 mutations	No
ALFRED (The ALlele FREquency Database)	Yale University	Allele frequency data for population studies	1,000 polymorphisms in 356 populations 20,000 frequency tables	No
Assays-on-Demand	Applied Biosystems	SNPs from dbSNP and Celera with frequency data. Public coordinates provided for many Celera SNPs. Need Celera license to see Celera data, of course.	160,000 SNPs	No
MutationDiscovery.com	Transgenomic	SNPs from dbSNP and some internally generated	24,000 loci 1.3 millions SNPs	No

Last modified May 5, 2004 by Nat Goodman