Tag: polymorphism

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public ...

dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations an ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular dia ...

The European Variation Archive is an open-access archive that accepts submission of, and provides access to, all types of genetic variation data from all species. All users are able to download any dataset, or query our study catalogue via our variat ...

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variat ...

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

LOINC is a common language (set of identifiers, names, and codes) for clinical and laboratory observations. LOINC is a catalog of measurements, including laboratory tests, clinical measures like vital signs and anthropomorphic measures, standardized ...

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can b ...

A text format devised by Ensembl for the eponymous Variant Effect Predictor tool.

dbVar is a database of human genomic structural variation where users can search, view, and download data from submitted studies. dbVar stopped supporting data from non-human organisms in 2017, however existing non-human data remains available. In ke ...

The Database of Genomic Variants (DGV) is a publicly accessible, comprehensive curated catalogue of structural variation (SV) found in the genomes of control individuals from worldwide populations.

The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature, databases and unpublished data.

MaizeGDB is the maize research community's central repository for genetics and genomics information.

DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) is an interactive web-based resource that incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversion ...

The Allele Frequency Net Database (AFND) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunogl ...

neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes.

The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...

The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in the Finnish population. It provides valuable summary data for researchers and clinicians as well as other researchers with an interest in gen ...

The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...

The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. ...

PolymiRTS (Polymorphism in microRNAs and their TargetSites) is a database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational ...

SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds pe ...

SNPedia is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). Curati ...

GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.

The profile hidden Markov Model (HMM) calculated from multiple sequence alignment data in this service is stored in Profile HMM save format (usually with ".hmm" extension). It is an ASCII file containing a lot of header and descriptive records follow ...

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes compara ...

A registry of Hereditary Auto-inflammatory Disorder Mutations.

miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mi ...

The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information ...

Autism genetics KnowledgeBase, an evidence-based knowledgebase of autism genetics.

The ITHANET Portal represents an expanding resource for clinicians and researchers dealing with haemoglobinopathies and a port of call for patients in search of professional advice. The ITHANET Portal integrates information on news, events, clinical ...

Selectome is a database of positive selection, based on a branch-site likelihood test. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees.

The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. The JGA contains exclusive data col ...

ALFRED is designed to make allele frequency data on human population samples readily available for use by the scientific and educational communities.

Retrotransposons, which comprises LINE, SINE and LTR-containing elements, accounts for almost half of our genome (Fig. 1). They are mobile genetics elements - also known as jumping genes - but only the L1-HS subfamily has retained the ability to jump ...

This guideline describes a set of best practices when using phenotype ontologies to annotate genomic variant files using Genome Variation Format (GVF) and the Sequence Ontology.

DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.

Polymorphic miRNA-mediated gene regulation in vertebrates

PMut Data Repository collects predictions of the pathological effect of all possible single amino acid variants on Uniref Human protein sequences. Predictions were prepared using PMut 2017 predictor (2017 version).

KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. This resources provides plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme ...

The dbDEPC is a database of differentially expressed proteins in human cancers.

The GrainGenes website hosts a wealth of information for researchers working on Triticeae species, oat and their wild relatives. The website hosts a database encompassing information such as genetic maps, genes, alleles, genetic markers, phenotypic d ...

The AlloMAPS database provides data on the energetics of communication in proteins with well-documented allosteric regulation, allosteric signalling in PDBselect chains, and allosteric effects of mutations. In addition to energetics of allosteric sig ...

An integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations.

A crowdsourced collection of personal genomics data. Includes SNP genotyping, exome sequencing data, phenotypic annotation and quantified self tracking data.

Satellog is a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism.

The Centre for Arab Genomic Studies (CAGS) initiated the ambitious project to establish the CTGA (Catalogue of Transmission Genetics in Arabs) database for genetic disorders in Arabs with the aim to enlighten the scientific community and the public o ...

Polymorphic inversions in the human genome

The YH database presents the entire DNA sequence of a Han Chinese individual, as a representative of Asian population. This genome, named as YH, is the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years.assembled bas ...

Indian Genetic Disease Database

The MMRRC distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community. The Catalog provides information on the strains ava ...

The chicken Variation Database (ChickVD) is an integrated information system for storage, retrieval, visualization and analysis of chicken variation data.

Mouse Indel Polymorphism Database

Drosophila Polymorphism Database, is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Drosophila genus. It allows, for the first time, the search for any polymorphic set according to different par ...

This ontology is used to model scientific investigation, especially Genome-Wide Association Studies (GWAS), to discover genetic susceptibility factors to disease, such as Diabetes. It models the genetic variants, polymorphisms, statistical measuremen ...

FINDbase (http://www.findbase.org) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disord ...

mirDNMR is a database for the collection of gene-centered background DNMRs obtained from different methods and population variation data. The database has the following functions: (i) browse and search the background DNMRs of each gene predicted by f ...

The IPD-NHKIR database provides a centralised repository for non-human KIR (NHKIR) sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immuno ...

The SNP Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. The S ...

denovo-db is a collection of germline de novo variants identified in the human genome. de novo variants are those present in children but not their parents.

Data using the VarioML standard can be integrated with the global library of purely genetic data. VarioML is a central prerequisite for effective modelling of phenotype data and genotype-to-phenotype relationships. It removes the obstacles to the eff ...

The Moroccan Genetic Disease Database (MGDD) collect and document mutations and frequencies of polymorphisms reported in the Moroccan population. The information in the MGDD allow researchers and clinicians to find mutations associated to a given dis ...

The Genome Variation Format (GVF) is a very simple file format for describing sequence alteration features at nucleotide resolution relative to a reference genome.

A curated database of mutations and polymorphisms associated with Lafora Progressive Myoclonus Epilepsy. The Lafora progressive myoclonus epilepsy mutation and polymorphism database is a collection of hand curated mutation and polymorphism data for t ...

The Type 2 Diabetes Knowledge Portal is an open-access resource for human genetic information on type 2 diabetes (T2D). It is a central repository for data from large genomic studies that identify DNA variants whose presence is linked to altered risk ...

Whole-genome sequence data, variant calls, and annotations of natural genetic variation in C. elegans species.

Various types of human gene polymorphism

Annotated SNPs within regulatory DNA elements

A compilation of human mutation databases

A database of recent positive selection across human populations

Disease-related non-synonymous mutations

dbRIP is a highly integrated database of Retrotransposon Insertion Polymorphism (RIPs) in human. It currently contains a non-redundant list of 1608 polymorphic Alus and 387 polymorphic L1s. In dbRIP, we deploy the utilities and genome annotation data ...

Functional effects of various human SNPs

Single Amino acid polymorphisms: SNP-derived variation in human proteins

VarySysDB Disease Edition: Disease-associated genomic polymorphisms

Topographic database of non-synonymous SNPs

Signature of selection in the human genomes

Interactive SNP annotation, selection and prioritization system for genotyping projects and/or analysis and interpretation of SNP data.

Disease mutations in the Cypriot population

Microsatellite markers genotyped in Taiwanese populations

List of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs.

JAX® Mice are the industry standard for animal model research, using precise genome solutions to better understand human disease. Our rigorous Animal Health Programs and stringent genetic quality standards ensure the reproducibility and validity of y ...

>>> !!! the repository is offline !!! The current successor is https://www.lovd.nl/USH1C. <<< The database contains all the variants published as pathogenic mutations in the international literature up to November 2007. In addition, unpublished Ushe ...

PhenomicDB is a multi-species genotype/phenotype database,integrating public genotype/phenotype data from a wide range of modelorganisms and Homo sapiens. Genotype and phenotype descriptions areobtained from Entrez Gene, OMIM, wormbase, flybase, and ...

The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for ...

The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more scalable MySQL engine. Users can access the data via ...

Lynx (http://lynx.ci.uchicago.edu)is a web-based database and a knowledge extraction suite of tools designed specifically to support the discovery and hypothesis-based approaches to identification of genetic factors contributing to phenotypes or diso ...

DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version is the first database indexing >1 million entries, corresponding to ~670 000 un ...