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Variations

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ktym edited this page May 19, 2014 · 14 revisions

SIO/GFVO/SO/GFF/GTF/GVF/VCF/INSDC/Ensembl table

Ensembl sources for variation data

name description
dbSNP Variants (including SNPs and indels) imported from dbSNP
Archive dbSNP Former variants names imported from dbSNP
LSDB Variants dbSNP annotates as being from LSDBs
PubMed Variants with pubmed citations
PhenCode PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans
ESP The goal of the NHLBI GO Exome Sequencing Project is to discover novel genes and mechanisms contributing to heart, lung and blood
HGMD-PUBLIC Variants from HGMD-PUBLIC dataset September 2013
dbPEX dbPEX, PEX Gene Database
KAT6BDB K(lysine) acetyltransferase 6B database, BCM
DGVa Database of Genomic Variants Archive
NHGRI_GWAS_catalog Variants associated with phenotype data from the NHGRI GWAS catalog
EGA Variants imported from the European Genome-phenome Archive with phenotype association
Uniprot Variants with protein annotation imported from Uniprot
OMIM Variations linked to entries in the Online Mendelian Inheritance in Man (OMIM) database
Open Access GWAS DB Johnson & O'Donnell 'An Open Access Database of Genome-wide Association Results' PMID:19161620
Illumina_CytoSNP12v1 Variants from the Illumina Cyto SNP-12 v1 whole genome SNP genotyping chip designed for cytogenetic analysis
Illumina_Human660W-quad Variants from the Illumina Human 660W-Quad whole genome SNP genotyping chip designed for association studies
Illumina_Human1M-duoV3 Variants from the Illumina Human 1M-DuoV3 whole genome SNP genotyping chip designed for association studies
Affy GenomeWideSNP_6 CNV Copy Number Variation (CNV) probes from the Affymetrix Genome-Wide Human SNP Array 6.0
COSMIC Somatic mutations found in human cancers from the COSMIC project
LSDB_PPIB PPIB homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database
LSDB_CRTAP CRTAP homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database
LSDB_LEPRE1 LEPRE1 homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database
LSDB_FKBP10 FKBP10 homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database
dbSNP_ClinVar Variants of clinical significance imported from dbSNP/ClinVar
DDG2P Developmental Disorders Genotype-to-Phenotype Database
GIANT The Genetic Investigation of ANthropometric Traits (GIANT) consortium is an international collaboration that seeks to identify g
OMIMGENE Online Mendelian Inheritance in Man (OMIM) database
Orphanet The portal for rare diseases and drugs
MAGIC MAGIC (the Meta-Analyses of Glucose and Insulin-related traits Consortium) represents a collaborative effort to combine data fro
HbVar A Database of Human Hemoglobin Variants and Thalassemias
LMDD Leiden Muscular Dystrophy Database
OIVD Osteogenesis Imperfecta Variant Database
PAHdb Phenylalanine hydroxylas database
Infevers The registry of Hereditary Auto-inflammatory Disorders Mutations
dbGaP The database of Genotypes and Phenotypes.
AMDGC The AMD Gene consortium is an international collaboration that seeks to identify genetic loci associated with age-related macula
GEFOS The GEnetic Factors for OSteoporosis Consortium international collaboration that seeks to identify common risk gene variants for
IIBDGC International Inflammatory Bowel Disease Genetics Consortium
Teslovich Biological, clinical and population relevance of 95 loci for blood lipids

Variations to phenotypes

NCBI dbSNP

NCBI ClinVar

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