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Variant-disease association databases | Genome variation analysis

The invention of high throughput sequencing technologies has led to the discoveries of hundreds of thousands of genetic variants associated with thousands of human diseases. Many of these genetic variants are located outside the protein coding…
OMIM
Dataset

OMIM Online Mendelian Inheritance in Man

A comprehensive, authoritative and timely research resource of curated…

A comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them. OMIM® is based on the published peer-reviewed…

EGA
Dataset

EGA European Genome-phenome Archive

A permanent archive that promotes the distribution and sharing of genetic and…

A permanent archive that promotes the distribution and sharing of genetic and phenotypic data consented for specific approved uses but not fully open, public distribution. The EGA follows strict…

DECIPHER
Dataset

DECIPHER DatabasE of Genomic variants and Phenotype in Humans Using Ensembl Resources

An accessible online repository of genetic variation with associated phenotypes…

An accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders.…

HGMD
Dataset

HGMD Human Gene Mutation Database

Represents an attempt to collate known (published) gene lesions responsible for…

Represents an attempt to collate known (published) gene lesions responsible for human inherited disease. HGMD® has been an essential tool in analyzing the genomes of thousands of individuals and is…

ClinVar
Dataset

ClinVar

Provides germline and somatic variants of any size, type or genomic location.…

Provides germline and somatic variants of any size, type or genomic location. ClinVar gathers interpretations of clinical significance of variants for reported conditions. It accepts submissions from…

LOVD
Dataset

LOVD Leiden Open Variation Database

Provide a flexible, freely available tool for Gene-centered collection and…

Provide a flexible, freely available tool for Gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data,…

iRegNet3D
Web

iRegNet3D

Integrates multiple regulatory networks and human disease-associated mutations…

Integrates multiple regulatory networks and human disease-associated mutations for the generation of mechanistic insights into pathogenesis. iRegNet3D can be used for understanding the mechanisms by…

LRG
Dataset

LRG Locus Reference Genomic

Gathers information about reference sequences designed for the reporting of…

Gathers information about reference sequences designed for the reporting of diagnostically relevant variants. Locus Reference Genomic (LRG) is a manually curated database which provides for each…

PolyDoms
Dataset

PolyDoms

Classifies and catalogs the predicted functionality of nonsynonymous coding…

Classifies and catalogs the predicted functionality of nonsynonymous coding SNPs (nsSNPs) in human genes to facilitate sequence-based association studies. PolyDoms contains a central table,…

VariantDB
Dataset

VariantDB

Provides unified broad annotation and flexible filtering strategies. VariantDB…

Provides unified broad annotation and flexible filtering strategies. VariantDB can retrieve annotation or filtering data from multiple sources in parallel. It can provide family and experimental…

MME API
Desktop

MME API Matchmaker Exchange Application Programming Interface

A protocol and data format for exchanging phenotype and genotype profiles to…

A protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate…

HIVheritability
Desktop

HIVheritability

Estimates the extents to which viral load is heritable either via the viral…

Estimates the extents to which viral load is heritable either via the viral genotype (from donor to recipient) or via the host’s Human Leukocyte Antigen (HLA) genotype. HIVheritability uses linear…

PhenCode
Dataset

PhenCode Phenotypes for ENCODE

A collaborative, exploratory project to help understand phenotypes of human…

A collaborative, exploratory project to help understand phenotypes of human mutations in the context of sequence and functional data from genome projects. PhenCode connects human phenotype and…

LSDBs
Dataset

LSDBs Locus-Specific DataBases

Store information on gene sequence variation associated with human phenotypes…

Store information on gene sequence variation associated with human phenotypes and are frequently used as a reference by researchers and clinicians. Their most frequent use is in relation to DNA-based…

PhID
Dataset

PhID

Gathers network pharmacology related interactions information at the systemic…

Gathers network pharmacology related interactions information at the systemic level. PhID aims to provides a repository for visualizing relationships between entities such as drugs, targets,…

Skeleton…
Dataset

Skeleton Genetics

The first comprehensive and annotated genetic skeletal disorders database,…

The first comprehensive and annotated genetic skeletal disorders database, which contains information about all genetic skeletal disorders-related knowledge. SkeletonGenetics includes 8225 mutations…

dbDSM
Dataset

dbDSM database of Deleterious Synonymous Mutation

Collects, curates and manages available human disease-related SM data obtained…

Collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289…

DIVAS
Dataset

DIVAS Disease Variant Store

Provides information on genetic variants observed in various disease…

Provides information on genetic variants observed in various disease populations. We have gathered several large studies, including GERA and GRU, and computed population- and disease-specific genetic…

PhenoDB
Dataset

PhenoDB

A robust, useful database for collection, storage, and analysis of phenotypic…

A robust, useful database for collection, storage, and analysis of phenotypic data, especially in the context of whole exome/genome sequencing approaches to identify the responsible gene and variant.…

GeneMatcher
Web

GeneMatcher

A freely accessible web-based tool developed as part of the Baylor-Hopkins…

A freely accessible web-based tool developed as part of the Baylor-Hopkins Center for Mendelian Genomics. The goal of GeneMatcher is to identify additional individuals with rare phenotypes who had…

Genotator
Web

Genotator

Integrates over a host of mainstream databases to provide automatic and…

Integrates over a host of mainstream databases to provide automatic and up-to-date information on any human disease. Genotator includes data from 11 externally accessible clinical genetics resources…

1-CMDb
Dataset

1-CMDb

Allows to interrogate associations between one-carbon metabolism genes and a…

Allows to interrogate associations between one-carbon metabolism genes and a host of human disorders. 1-CMDb provides a collection of genes, associated polymorphisms and genetic variations in genomic…

eRAM
Dataset

eRAM encyclopedia of Rare disease Annotations for Precision Medicine

Provides a resource for researchers and clinicians to conduct studies and…

Provides a resource for researchers and clinicians to conduct studies and practice in rare diseases. eRAM is an online resource that includes (i) collected phenotypes and symptoms of rare diseases…

COGR
Dataset

COGR Canadian Open Genetics Repository

A unified, open-access, clinical-grade genetic database that draws from the…

A unified, open-access, clinical-grade genetic database that draws from the genetic holdings in place at clinical labs and hospitals across Canada. As clinical laboratories adopt modern genomics…

PhenomeCentral
Dataset

PhenomeCentral

A repository for secure data sharing targeted to clinicians and scientists…

A repository for secure data sharing targeted to clinicians and scientists working in the rare disorder community. PhenomeCentral encourages global scientific collaboration while respecting the…

Cafe Variome
Dataset

Cafe Variome

A complete data sharing solution designed to allow diagnostic/disease networks…

A complete data sharing solution designed to allow diagnostic/disease networks to share variant data between one another, for example to check for the existence of variant found in a patient in…

SNP2Structure
Dataset

SNP2Structure

Annotates mutated positions both in protein sequences and their associated…

Annotates mutated positions both in protein sequences and their associated X-ray and solution nuclear magnetic resonance (NMR) structures. SNP2Structure allows users to inspect protein mutations that…

Genatlas
Dataset

Genatlas

Contains a collection of 22853 genes, 5851 phenotypes and 138291 citations from…

Contains a collection of 22853 genes, 5851 phenotypes and 138291 citations from human diseases. Genatlas provides mapping, structural and functional information on genes and associated diseases. The…

DistiLD Database
Dataset

DistiLD Database DistiLinkage Disequilibrium Database

Increases the usage of existing genome-wide association study (GWAS) results.…

Increases the usage of existing genome-wide association study (GWAS) results. DistiLD database performs three important tasks: (i) published GWAS are collected from several sources and linked to…

dbWGFP
Dataset
PTM-SNP
Dataset

PTM-SNP

Contains a comprehensive collection of human non-synonymous SNPs (nsSNPs) that…

Contains a comprehensive collection of human non-synonymous SNPs (nsSNPs) that affect post-translational modification (PTM) sites, together with disease information. Total 179,325 PTM-SNPs were…

TCLP
Dataset

TCLP TRON Cell Line Portal

Allows users to search and list gene expression values from a selected cell…

Allows users to search and list gene expression values from a selected cell line. TCLP integrates a catalog of cancer cell line annotations integrating human leukocyte antigen (HLA) type, HLA…

CNVD
Dataset

CNVD Copy Number Variation in Disease

A systematic and comprehensive database for copy number variations and related…

A systematic and comprehensive database for copy number variations and related diseases, in which all the records were manually extracted from experimental data published in CNV-related articles.…

PRO-MINE
Web

PRO-MINE PROtein Mutations In NEurodegeneration

Contains data from the literature regarding all TDP-43/TDP43/TARDBP gene…

Contains data from the literature regarding all TDP-43/TDP43/TARDBP gene disease-associated mutations identified to date. PRO-MINE provides a web interface to query the database and to provide tools…

HGDP
Dataset

HGDP Human Genome Diversity Project

Allows to genetic diversity in human populations. HGDP has collected genomic…

Allows to genetic diversity in human populations. HGDP has collected genomic DNA from 1,043 individuals from around the world and has determined their genotypes at more than 650,000 single nucleotide…

CNV association DB
Dataset

CNV association DB Copy Number Variation association Database

Informs about copy number variation (CNV) association. CNV association DB is an…

Informs about copy number variation (CNV) association. CNV association DB is an online resource that puts in storage CNV region data, or results of one research laboratory. The database can be browse…

G T A T C G C T A
HLA DB
Dataset

HLA DB HLA Database

Holds information about human leukocyte antigen (HLA). HLA DB is a repository…

Holds information about human leukocyte antigen (HLA). HLA DB is a repository system containing HLA haplotype data and disease-related information. This resource can be browse by two ways: (1) a…

iBinom
Web

iBinom

Allows scientists to analyse genome information for inherited disease…

Allows scientists to analyse genome information for inherited disease diagnostics. iBinom is compatible with the most popular sequencing instrument specification and all results are reproducible. It…

Ranomics
Dataset

Ranomics

Helps to determine functionally-characterized genetic variants role in disease…

Helps to determine functionally-characterized genetic variants role in disease development and treatment. Ranomics is a comprehensive database that founded on one core principle: to improve…

MyGene2
Dataset

MyGene2

Offers a portal through which families with rare genetic conditions who are…

Offers a portal through which families with rare genetic conditions who are interested in sharing their health and genetic information can connect with other families, clinicians, and researchers. By…

IGVBrowser
Dataset

IGVBrowser

Provides allele and genotype frequency data generated in the Indian Genome…

Provides allele and genotype frequency data generated in the Indian Genome Variation Consortium (IGVC) project. The database harbors 4,229 SNPs from more than 900 candidate genes in contrasting…

Genome Trax
Dataset

Genome Trax

A comprehensive compilation of variant knowledge that is made available for…

A comprehensive compilation of variant knowledge that is made available for download for easy integration into your own custom variant analysis pipeline for human whole genome, exome and targeted…

Exome Variant…
Dataset

Exome Variant Server

The NHLBI Exome Sequencing Project (ESP) is focused on understanding the…

The NHLBI Exome Sequencing Project (ESP) is focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped…

GeneReviews
Dataset

GeneReviews

A collection of peer-reviewed inherited disease descriptions written by experts…

A collection of peer-reviewed inherited disease descriptions written by experts with extensive and thoughtful editing. It contains phenotypic information and information on selected variants, and its…

Cancer GAMAdb
Dataset

Cancer GAMAdb Genome-wide Association and Meta Analyses database

Contains key descriptive characteristics of each genetic association extracted…

Contains key descriptive characteristics of each genetic association extracted from published genome-wide association studies (GWAS) and meta-analyses relevant to cancer risk. Cancer GAMAdb is a…

HUMSAVAR
Dataset

HUMSAVAR

An index of human polymorphisms and disease mutations. In release 2015_08 of…

An index of human polymorphisms and disease mutations. In release 2015_08 of July 2015, the total number of single amino acid variants annotated in UniProtKB/Swiss-Prot was 71,795. All are listed in…

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