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From Variome
Variome.net: difference among individuals and populations in one species.
The variome.net is an openfree web resource and encyclopedia of world wide SNP (Single Nucleotide Polymorphism) researchers. The variome.net aims to support the international genome variance researches by collecting, organizing, analyzing, and disseminating variome information.
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Worldwide Variome Project
What are Variome and Variomics?:
Are humans a single species?
Current Research (Please list your projects here)
- Applications
Service Opened!
- SNP@Web : SNP database and tool catalogs http://variome.kobic.re.kr/SNPatWEB/
- SNP@Domain : A web resource of Single Nucleotide Polymorphisms (SNPs) within protein domain structures and sequences http://variome.kobic.re.kr/SnpNavigator/
- SNP@Ethnos : A database of Ethnically Variant SNPs http://variome.kobic.re.kr/SNPatETHNIC/
- SNP@Promoter (NEW!): A web resource of Single Nucleotide Polymorphisms (SNPs) within promoter. http://variome.kobic.re.kr/SNPatPromoter
- SNP2NMD : A database of human SNPs resulting NMD PTC. http://variome.kobic.re.kr/SNP2NMD
- SNP2SPLICE (Updating!): A database of Single Nucleotide Polymorphisms within splicing sites.
- FESD : A web-based integrated database for selecting sets of SNPs in putative functional elements in human gene http://variome.kobic.re.kr/FESD
- Alternatome (Updating!) : A database of alternative splicing with splicing array to understand gene regulation.
Under development!
- MitoVariome: A database for variation on mitochondria
Infra Resources
from (KOBIC).
SNPpipe: a collection of automatic downloading and parsing modules Website
Web Resources
from (KOBIC).
- [PUBLISHED]
SNP@Promoter http://variome.kobic.re.kr/SNPatPromoter/
: Human SNP databases for transcription regulatory regions. http://www.biomedcentral.com/1471-2105/9/S1/S2
- [PUBLISHED]
SNP2NMD http://variome.kobic.re.kr/SNP2NMD/
: A database of human SNPs causing NMD (nonsense-mediated mRNA decay). http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/3/397
- [PUBLISHED]
SNP@Ethnos http://variome.kobic.re.kr/SNPatETHNIC/
: A database of Ethnically Variant SNPs.
http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D711
- [PUBLISHED]
SNP@Domain http://variome.kobic.re.kr/SnpNavigator/ or http://snpnavigator.net/
: A web resource of Single Nucleotide Polymorphisms (SNPs) within protein domain structures and sequences.
http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W642
- [PUBLISHED]
D2SNP http://bioportal.kobic.re.kr:8080/D2GSNP/index.faces
: A web-based tools for the selection of a set of SNPs within candidate genes of human diseases.
http://www.kogo.or.kr/bulletin/UploadFile/rapidcom_1_200603.pdf
- [PUBLISHED]
FESD http://variome.kobic.re.kr/FESD
: A web-based integrated database for selecting sets of SNPs in putative functional elements in human gene.
http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D518
Research results
from (KOBIC).
- [PUBLISHED]
Comparative study of the linkage disequilibrium of an ENCODE region, chromosome 7p15, in Korean, Japanese, and Han Chinese samples.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16376517
Global Project Links
HVP : Human Variome Project
Broadly External Links
a PASNP site: Pan Asia SNP project related site.
Biopedia,
siphs:a life sciences community,
Medicine and molecular biology DB
dbGap: a Database of Genome Wide Association Studies
FESTA tagSNP picker
Haplo, Haplot
Allele Frequency Database at Yale. USA
Q & A
Opinions
Meetings and conferences
International Meetings on Variome
SNP Basics
- SNPs: Variations on a Theme - A basic introduction to SNPs from the National Center for Biotechnology Information (NCBI).
- Understanding SNPs and Cancer - An online tutorial from the National Cancer Institute.
- Diseases and Medical Response - An animated tutorial describing how DNA markers are used in medical applications. Part of the Kids Genetics Web site from GlaxoSmithKline.
- Genome Variations - Questions and answers about genome variation from the Genome News Network.
- The Cutting Edge: SNPs and Their Medical Application - From The Wellcome Trust.
- A Brief Guide to SNPs - A set of questions and answers from The Wellcome Trust.
Variome Server - http://variome.kobic.re.kr
Variome tools
PLINK
Members (everyone is welcome to participate in)
- Areum Han
- Sung Sam Gong
- Yubok Cho
- Hyo Jin Khang
- Jong Bhak: Jong is a bioinformatist living in Asia now.
- Sohyun Hwang
- Woo-Yeon Kim
- Jin Ok Yang
- Ho Ghang
1. Prichard et al, 2000, Inference of Population Structure Using Multilocus Genotype Data, Genetics, 155, 945-959.
2. Bowcock et al, 1994, High resolution of human evolutionary trees with polymorphic microsatellites, Nature, 368, 31, 455-457.
3. Shriver et al, 2004, The genome distribution of population substructure in four populations using 8,524 autosomal SNPs.
4. Shriver et al, 2005, Large-scale SNP analysis reveals clustered and continuous patterns o f human genetic variation.
5. Adeyemo et al, 2005, Genetic structure in four West African population groups.
6. Chakraborty and Jin, 1993, A unified approach to study hypervariable polymorphisms: Statistical considerations of determining relatedness and population distances.
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