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Rare and low-frequency variation databases | Genome variant analysis

Databases of genetic variation are important for our understanding of human population history and biology (Fu et al., 2013; The 1000 Genomes Project Consortium, 2015; Li and Durbin, 2011; Stoneking and Krause, 2011; MacArthur et al., 2012) but also…
Ensembl
Dataset

Ensembl

A genomic interpretation system providing the most up-to-date annotations,…

A genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. The REST server, which allows programs written in…

IGSR
Dataset

IGSR International Genome Sample Resource

Expands in data type and population diversity the resources from the 1000…

Expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these…

International…
Dataset

International HapMap Project

A multi-country effort to identify and catalog genetic similarities and…

A multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health,…

VarSome
Dataset

VarSome

A knowledge base and aggregator for human genomic variants. VarSome gives fast…

A knowledge base and aggregator for human genomic variants. VarSome gives fast access to more than 17 billion items of variant and gene annotation sourced from public databases. It also provides…

dbSNP
Dataset

dbSNP

A variation database at the National Center for Biotechnology Information…

A variation database at the National Center for Biotechnology Information (NCBI). dbSNP is a public repository of submitted nucleotide variations and is part of NCBI's search and retrieval…

TriTrypDB
Dataset

TriTrypDB

Provides information about Trypanosomatidae. Tritrypdb is a collective database…

Provides information about Trypanosomatidae. Tritrypdb is a collective database which intends to gather annotation, curation and access to tools enabling sophisticated queries against genomic scale…

UK10K
Dataset

UK10K

A WGS imputation panel comprising 3,781 samples from the UK10K Cohorts project.…

A WGS imputation panel comprising 3,781 samples from the UK10K Cohorts project. This project has generated a data set of 3,781 whole genomes sequenced at low depth aiming to exhaustively characterize…

DGV
Dataset

DGV Database of Genomic Variants

Provides a comprehensive summary of structural variation in the human genome.…

Provides a comprehensive summary of structural variation in the human genome. We define structural variation as genomic alterations that involve segments of DNA that are larger than 50bp. The content…

CryptoDB
Dataset

CryptoDB

Compiles information about Cryptosporidium. Cryptodb intends to collect whole…

Compiles information about Cryptosporidium. Cryptodb intends to collect whole genome sequence, annotation, sequence analysis and related data about this parasite. The database integrates a set of…

ExAC browser
Web
Desktop

ExAC browser

A lightweight, flexible browser framework to display large population datasets…

A lightweight, flexible browser framework to display large population datasets of genetic variation. ExAC browser provides gene- and transcript-centric displays of variation, a critical view for…

UMD-BRCA1/BRCA2
Dataset

UMD-BRCA1/BRCA2 Universal mutation database-BRCA1/BRCA2

Provides exhaustive databases of French BRCA1/2 variants. UMD-BRCA1/BRCA2 is…

Provides exhaustive databases of French BRCA1/2 variants. UMD-BRCA1/BRCA2 is divided into six sections, four of which are dedicated to information on the BRCA1 or BRCA2 genes and numbering of exons…

ToxoDB
Dataset

ToxoDB

A genome and functional genomic database for the protozoan parasite Toxoplasma…

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii.

DGVa
Dataset

DGVa Database of Genomic Variants archive

A repository that provides archiving, accessioning and distribution of publicly…

A repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. The DGVa accepts direct submissions from researchers and…

DbVar
Dataset

DbVar

A database of genomic structural variation. DbVar contains insertions,…

A database of genomic structural variation. DbVar contains insertions, deletions, duplications, inversions, multinucleotide substitutions, mobile element insertions, translocations, and complex…

mirDNMR
Dataset

mirDNMR

Collects gene-centered background De Novo Germline Mutation Rates (DNMRs)…

Collects gene-centered background De Novo Germline Mutation Rates (DNMRs) obtained from different methods and population variation data. MirDNMR provides the following functions: (i) browse and…

Platinum…
Dataset

Platinum Genomes

A genome-wide catalogue of 5.4 million “platinum” variants. We generated…

A genome-wide catalogue of 5.4 million “platinum” variants. We generated deep, whole-genome sequence data of seventeen individuals in a three-generation pedigree and called variants in each…

DrosDel…
Dataset

DrosDel deletion collection

Contains molecularly mapped deletions on an isogenic background. DrosDel…

Contains molecularly mapped deletions on an isogenic background. DrosDel deletion collection is a drosophila genomewide chromosomal deficiency resource that facilitates selection of other mapped…

PigVar
Dataset

PigVar

Contains high density pig whole-genome wide variation data and positive…

Contains high density pig whole-genome wide variation data and positive selection calls using genome data from three broad pig populations: Chinese domestic pigs, Tibetan pigs and European domestic…

Kaviar
Web

Kaviar Known VARiants

Allows user to assess novel variants. Kaviar is a compilation of human single…

Allows user to assess novel variants. Kaviar is a compilation of human single nucleotide variants (SNVs) collected from many and diverse sources. It is interested by known variants and genomic…

HUMA
Dataset

HUMA Human Mutation Analysis

Provides a platform for analyzing variation. The HUMA interface includes tools…

Provides a platform for analyzing variation. The HUMA interface includes tools to analyze variation in protein sequence and structures. It contains information about sequence, structure, variation…

dbDNV
Dataset

dbDNV DNV Database

Collects nucleotide variants of duplicated gene loci (DGL) in the human…

Collects nucleotide variants of duplicated gene loci (DGL) in the human reference genome via sequence alignments. dbDNV is a database that offers the browsing function and allows different queries in…

A A A
LncVar
Dataset

LncVar Long noncoding Variation

A database of genetic variation associated with long noncoding genes in 6…

A database of genetic variation associated with long noncoding genes in 6 species. The LncVar database can be used as a resource to evaluate the effects of the variations on the biological function…

A Catalog of…
Dataset

A Catalog of Human STR Variation

A catalog of STR variation using over 1000 individuals from the 1000 Genomes…

A catalog of STR variation using over 1000 individuals from the 1000 Genomes Project. It provides data on close to 700,000 STR loci, which encompasses 97% of the STRs with motifs of 2–6 bp in the…

CNVVdb
Dataset

CNVVdb

Provides potential inter-species copy number variations (CNV) information.…

Provides potential inter-species copy number variations (CNV) information. CNVVdb is a database that allows users to find duplicated regions within a genome (paralogues) and between different genomes…

InvFEST
Dataset

InvFEST

A database combining multiple sources of information to generate a complete…

A database combining multiple sources of information to generate a complete catalogue of non-redundant human polymorphic inversions. Due to the complexity of this type of changes and the underlying…

GVM
Dataset

GVM Genome Variation Map

Gathers information about genome variations. GVM is an online resource that…

Gathers information about genome variations. GVM is an online resource that allows users to obtain data on single nucleotide polymorphisms (SNPs) and small insertions and deletions (INDEL), with…

HGVA
Dataset

HGVA Human Genome Variation Archive

Allows to access to key and high-quality reference project data. HGVA is a…

Allows to access to key and high-quality reference project data. HGVA is a genetic variation resource which contains variants from key world-wide reference projects and added-value information as…

denovo-db
Dataset

denovo-db

Contains data about human de novo variants. The Denovo-db features include…

Contains data about human de novo variants. The Denovo-db features include different variant informations like chromosome location, change, or type. The website of denovo-db includes a feature…

COPA
Desktop

COPA Cancer Outlier Profile Analysis

Finds genes undergoing recurrent fusion in a given cancer type by finding pairs…

Finds genes undergoing recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. COPA is intended to find pairs of genes that may be involved in…

CHOP CNV
Dataset

CHOP CNV

A data set consisting primarily of relatively rare human genomic CNVs that were…

A data set consisting primarily of relatively rare human genomic CNVs that were derived from 2026 healthy individuals using high-density, SNP-based oligonucleotide microarrays. The generation of this…

VariSNP
Dataset

VariSNP

A benchmark database suite comprising variation datasets that can be used for…

A benchmark database suite comprising variation datasets that can be used for developing and testing the performance of variant effect prediction tools. VariSNP contains datasets selected from dbSNP…

DiscovEHR
Dataset

DiscovEHR

Provides a blueprint for large-scale precision medicine initiatives and…

Provides a blueprint for large-scale precision medicine initiatives and genomics-guided therapeutic discovery. DiscovEHR is a browser which contains variant frequency data to enable allele frequency…

MutationalPatte…
Desktop

MutationalPatterns

A package to explore and visualize a collection of mutational patterns that are…

A package to explore and visualize a collection of mutational patterns that are relevant for deciphering which mutational processes have been active in a sample. MutationalPatterns facilitates both…

TMC-SNPdb
Dataset

TMC-SNPdb Tata Memorial Centre-SNP database

A database of ‘normal’ germline variants derived from Indian (nonEuropean…

A database of ‘normal’ germline variants derived from Indian (nonEuropean Caucasian population). TMC-SNPdb is the first open source, flexible, upgradable, and freely available single nucleotide…

SNPlocs.Hsapien…
Dataset

SNPlocs.Hsapiens.dbSNP.GRCh

Covers single nucleotide polymorphism (SNP) locations and alleles for Homo…

Covers single nucleotide polymorphism (SNP) locations and alleles for Homo sapiens. SNPlocs.Hsapiens.dbSNP.GRCh38 was constructed from NCBI dbSNP Build 150 and concerns reference genome GRCh38.p7.

FDb.UCSC.snpcom…
Dataset

FDb.UCSC.snpcommon.hg

Covers dbSNP build 137 and genome assembly hg19.

Covers dbSNP build 137 and genome assembly hg19.

Vancouver…
Desktop

Vancouver Short Read Analysis

A package for collating and searching across thousands of next-generation…

A package for collating and searching across thousands of next-generation sequence (NGS) samples. Vancouver Short Read Analysis provides a database can be installed easily to rapidly access and store…

CerealsDB
Dataset

CerealsDB

An online resource containing a range of genomic datasets for wheat (Triticum…

An online resource containing a range of genomic datasets for wheat (Triticum aestivum) that will assist plant breeders and scientists to select the most appropriate markers for marker assisted…

Neal’s DNA…
Dataset

Neal’s DNA Mutation Site

Provides databases and softwares for analyzing mutations at the transgenic and…

Provides databases and softwares for analyzing mutations at the transgenic and bacterial lacI gene, human p53 gene and hprt gene as well as transgenic lacZ gene.

SNP Control…
Dataset

SNP Control Database

Collects information related to single-nucleotide polymorphism (SNP) genome.…

Collects information related to single-nucleotide polymorphism (SNP) genome. SNP Control Database makes available information to assist user in evaluation of appropriate thresholds of quality…

CNV DB
Dataset

CNV DB Copy Number Variation Database

Handles copy number variation (CNV) data. CNV DB is a resource that includes…

Handles copy number variation (CNV) data. CNV DB is a resource that includes information about CNV region data and also results concerning research laboratory. The online platform offers several…

EVA
Dataset

EVA European Variation Archive

Offers a collection of genetic variation data for all species. EVA is…

Offers a collection of genetic variation data for all species. EVA is searchable by study, gene, chromosomal location or Single Nucleotide Polymorphism database (dbSNP) identifier. It works in…

Human…
Dataset

Human Chromosome 21 SNP Database

Provides integrated single nucleotide polymorphism (SNP) information about…

Provides integrated single nucleotide polymorphism (SNP) information about Human Chromosome 21 genes. The Human Chromosome 21 SNP database has integrated SMART database and Entrez dbSNP. The database…

Varietas
Dataset

Varietas

A genetic variation database that can be used for batch annotation of minor…

A genetic variation database that can be used for batch annotation of minor genomic variations, mainly single nucleotide polymorphisms (SNPs). Data is integrated from various sources, such as dbSNP,…

HGSVP
Dataset

HGSVP Human Genome Structural Variation Project

A catalogue of human genomic polymorphisms ascertained by experimental and…

A catalogue of human genomic polymorphisms ascertained by experimental and computational analyses. This database includes large-scale structural variation (LSV), copy number polymorphisms (CNPs) and…

PlasmoDB
Dataset

PlasmoDB

Provides a resource for data analysis and visualization in a gene-by-gene or…

Provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB is a functional genomic database for Plasmodium spp. It belongs to a family of genomic…

GiardiaDB
Dataset

GiardiaDB

A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the…

A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the WBC6 clinical isolate of G. lamblia. It is accessed via the standard EuPathDB web interface, providing a wide variety…

FungiDB
Dataset

FungiDB

A functional genomic resource for pan-fungal genomes that was developed in…

A functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center.

AmoebaDB
Dataset

AmoebaDB

Functional genomic databases serving the amoebozoa research communities.

Functional genomic databases serving the amoebozoa research communities.

MicrosporidiaDB
Dataset

MicrosporidiaDB

Functional genomic databases serving the microsporidia research communities.

Functional genomic databases serving the microsporidia research communities.

FESD
Dataset

FESD Functional Element SNPs Database

Provides categorizing functional elements in human genic regions and their…

Provides categorizing functional elements in human genic regions and their associated flanking sequences. FESD allows users to select a set of Single Nucleotide Polymorphism (SNPs) for gene-based…

SchistoDB
Dataset

SchistoDB

Provides a rich resource of genomic data for key blood flukes (genus…

Provides a rich resource of genomic data for key blood flukes (genus Schistosoma) which cause disease in hundreds of millions of people worldwide.

MouseIndelDB
Dataset

MouseIndelDB Mouse Indel Polymorphism Database

Gathers data about genomic indel polymorphisms. MouseIndelDB is an integrated…

Gathers data about genomic indel polymorphisms. MouseIndelDB is an integrated searchable database that presents high-resolution information about indel polymorphisms that distinguish inbred mouse…

PiroplasmaDB
Dataset

PiroplasmaDB

A genome database for the genus Piroplasma. PiroplasmaDB is a member of…

A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.

dbProP
Dataset

dbProP Protein Polymorphism database

Provides information on amino acid polymorphisms and splicing variants found in…

Provides information on amino acid polymorphisms and splicing variants found in protein coding region. dbProP is a protein polymorphism database that includes alternatively spliced transcript…

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