Home
Home Page for the UCSD SNP Discovery programs
PPG
Program
PPG program aims, organization,
projects, personnel, flow
chart
Program
Data
Public Data and UCSD Account Data
Human
Chromosomes
Human Genome info
Candidate
Loci
Mouse
Chromosomes
Mouse Genome info
Cand
Loci Homologues
SNPs
and Haplotypes
Single Nucleotide Polymorphism and Haplotype info
Usage
Usage and help for Program software
A. Primary SNP Resource Centers:
NCBI - National Center for Biotechnology Information,
USA
- Entrez SNP - dbSNP incorporated
into NCBI Entrez system
- dbSNP - Database of Single Nucleotide Polymorphisms; Build 122
- Mutations DBs - OMIM Locus-specific mutation database links
- dbSNP - Database of Single Nucleotide Polymorphisms; Build 122
UCSC Genome Bioinformatics - Univ Cal Santa Cruz, CA, USA
Note: A SNP track (based on dbSNP) is not yet available at UCSC for human assembly hg17 (May 2004)
- Genome Browser - zooms
and scrolls over Chromosomes
- Gene Sorter - expression, homology, and other info on groups of genes
- Blat - maps your sequence to the Genome
- Table Browser - access to the underlying Database (not for the timid ...)
- Gene Sorter - expression, homology, and other info on groups of genes
SNPs and Haplotypes
Haplotype Specs
- dbSNP
Recent
Changes
Changes in Web Site Data
DNASYSTEM
Web pages with Links to other Bioinformatic Sites
Ensembl - EMBL-EBI and Sanger Institute project for human
genome data
Note: use URL info for Ensembl links below to determine how to search for a given locus or object at Ensembl
- Site
Map - Ensembl Site Map for human information
- Ensembl SNP Report - NCBI dbSNP Info in SNPView, for CHGA (SNP rs729940, C/T, Arg381Trp)
- Ensembl Gene SNP Report - Gene SNP Report in GeneSNPView, for CHGA (gene ENSG00000100604)
- CEPH Haplotype Report - Ensembl Haplotype Info in HaploView, for RPL3 region (haplotype ID CHR22_A_61)
- Ensembl Disease Report - Disease Info in DiseaseView, for "Hypertension, essential" (loci AGTR1, AGTR1A, AT2R1, GNB3)
- Ensembl SNP Report - NCBI dbSNP Info in SNPView, for CHGA (SNP rs729940, C/T, Arg381Trp)
The
SNP Consortium (TSC) Ltd -
SNP Consortium at CSH: About;
News
GeneSNPs - Environmental Genome Project (EGP) data resource
at Utah
JSNP
Database - IMS-JST Japanese
SNP database, in Tokyo: Mission;
News
- SnpMap - SNP Info via
Snpmap at JSNP, for CHGA
- Human
SNP Database - Whitehead Institute,
MIT, database site; Description
- SNP Fact Sheet - Fact sheet about SNPs, from DOE Genomes at Oak Ridge (ORNL)
- Nickerson Group - Web site for Debbie Nickerson lab
- Environmental Genome Project (EJP) - the NIEHS Environmental Genome Project at WashU
- DNA Polymorphism Discovery Resource - Cell Lines and DNA Samples at Coriell Institute
- HGVbase - Human Genome Variation Database - European SNP database
- Human Mutation Databases/Resources - Amos Bairoch's (ExPASy) links
- SIMP (SNP Info Mining Pipeline) - Tools for SNP data mining, U. Chicago
- SNP - here's to independence and freedom !
- SNP - here's to the big trees, yet another SNP site !!
- SNP Fact Sheet - Fact sheet about SNPs, from DOE Genomes at Oak Ridge (ORNL)
C. Primary Haplotype Mapping Resource Centers:
International
HapMap Project - HapMap Project,
web site at CSH: About;
News
- HapMap Project Data -
browse, download, ENCODE, examine HapMap data
- GBrowse - hapmap browsing webpage at CSH; browse by entering objects, eg CHGA
International
HapMap Project - HapMap Project,
web site at NHGRI, NIH
Haplotype
Specifications - Development
of hap specs (HapMap) in dbSNP at NCBI
- Sample HapSet - Example
of NCBI Haplotype Data (Handle DBMHC)
- Sample Individual - Individual 3 from the above Sample HapSet (handle DBMHC)
D. Additional Haplotype Sites:
- UCSF-WU HapMap Project
- efforts on the International HapMap Project at WU and UCSF
Latest modification: November,
2004
If you have comments or queries, send email to Doug Smith