Bioinformatic Resources

  1. GWAS Catalog (https://www.ebi.ac.uk/gwas/):

    The NHGRI-EBI Catalog of human genome-wide association studies. As of 12/21/2022, the GWAS Catalog contains 6,180 publications and 458,152 associations.

  2. PheWAS (https://phewascatalog.org/):
    PheWAS analyze many phenotypes compared to a single genetic variant (or other attribute).

  3. PheWeb (https://pheweb.org/)
    The PheWeb instance populated with the UK Biobank summary statistics displays 28 million genetic markers assessed across 1,403 binary traits for 408,961 white British participants.

  4. Open Target Genetics (https://genetics.opentargets.org/):

    Open Target Genetics is a tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets.

  5. Open Target Platform (https://platform.opentargets.org/):

    The Platform provides a framework to allow the interactive or programmatic interrogation of target-disease evidence.

  6. HuGeAMP, T1DKP, AMP-AD, etc (https://kp4cd.org/):

    The Human Genetics Amplifier (HuGeAMP) is a software platform and infrastructure that aggregates, integrates, and analyzes human genetic and genomic data to spark insights into complex diseases.

  7. RegulomeDB (https://regulomedb.org/regulome-search/):

    RegulomeDB is a database that annotates SNPs with known and predicted regulatory elements in the intergenic regions of the H. sapiens genome.

  8. UK Biobank (https://www.ukbiobank.ac.uk/):

    UK Biobank is a population-scale (~500,000 participants) biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants.

  9. GEO, NCBI (https://www.ncbi.nlm.nih.gov/geo/):

    Gene expression Omnibus (GEO) is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted.

  10. ArrayExpress, EMBL-EBI (https://www.ebi.ac.uk/arrayexpress/):

    ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.

  11. ENCODE Project (https://www.encodeproject.org/):

    The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

  12. Single Cell Immune Profiling, 10X Genomics (https://www.10xgenomics.com/resources/datasets):

    20k Human PBMCs, 5' HT v2.0: Human peripheral blood mononuclear cells (PBMCs) of a healthy female donor aged 25-30 were obtained by 10x Genomics from AllCells.

Aging Genetics

  1. AgeAnno (https://relab.xidian.edu.cn/AgeAnno/#/):

    AgeAnno is a comprehensive and curated database, aiming to provide comprehensive chracterizations for aging-related genes across tissue-cell types in human by using single-cell RNA and ATAC sequencing data (scRNA and scATAC).

  2. HAGR (http://genomics.senescence.info/):

    Six core DBs that are manually curated by experts and regularly updated to ensure high quality data: GenAge, AnAge, GenDR, LongevityMap, DrugAge, and CellAge

  3. SynergyAge (https://www.synergyage.info/):

    A DB containing manually curated data, extracted from experimental studies, regarding gene combinations that affect lifespan. Genetic and lifespan data for three animal models (C. elegans, D. melanogaster and M. musculus) obtained through multiple longevity-modulating interventions.

  4. MetaboAge (https://www.metaboage.info/):
    A DB specialized in aging metabolomics that contains 408 metabolites in human extracted from 72 references.

  5. Open Genes (https://open-genes.com/genes):
    Open Genes provides detailed structured data for each experiment binding the gene and aging. This database is manually collected on gene evolution.

Gene/lncRNAs

  1. GENCODE (https://www.gencodegenes.org/):

    The goal of the GENCODE project is to identify and classify all gene features in the human and mouse genomes with high accuracy based on biological evidence, and to release these annotations for the benefit of biomedical research and genome interpretation.

  2. lncRNASNP2 (http://bioinfo.life.hust.edu.cn/lncRNASNP#!/):
    LncRNASNP is a database providing comprehensive resources of single nucleotide polymorphisms (SNPs) in human/mouse lncRNAs.

Linkage Disequilibrium

  1. 1000 Genomes Project, IGSR (https://www.internationalgenome.org/):

    The 1000 Genomes Project created a catalogue of common human genetic variation, using openly consented samples from people who declared themselves to be healthy.

  2. LDlink (https://ldlink.nci.nih.gov/?tab=home):

    LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups from the phase 3 haplotype data of the 1000 genomes Project.

  3. TopLD (http://topld.genetics.unc.edu/index.php):
    Providing linkage disequilibrium inferred with WGS data from 15,578 individuals in the NHLBI TOPMed program

Epigenetic marks

  1. Roadmap Epigenomics Project (https://egg2.wustl.edu/roadmap/web_portal/):

    The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research.

  2. SCREEN, ENCODE (https://screen.encodeproject.org/):
    SCREEN allows users to explore cis-Regulatory Elements (cCREs) and investigate how they connect with other annotations in the Encyclopedia in a cell-type-specific manner, as well as the underlying raw ENCODE data whenever available.

  3. wgEncodeRegTfbs (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeRegTfbsClustered/):
    Transcription factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs

  4. EpiMap (http://compbio.mit.edu/epimap/):
    We aggregated and uniformly re-processed 3,030 references from ENCODE, Roadmap, and GGR, and imputed 14,952 datasets across 859 biosamples and 18 marks/assays, which we report here as EpiMap (for Epigenome Integration across Multiple Annotation Projects).

  5. DHSlist (https://www.meuleman.org/research/dhsindex/):
    We created high-resolution maps of DNase I hypersensitives (DHSs) from 733 human biosamples encompassing 438 cell and tissue types and states, and integrated these to delineate and numerically index approximately 3.6 million DHSs within the human genome sequence, providing a common coordinate system for regulatory DNA.

  6. CATlas (http://catlas.org/catlas_hub/):
    Comprehensive atlas for regulatory elements and functional annotations: ~1.2M candidate cis-regulatory elements across 222 adult/fetal human tissue cell types

  7. FANTOM5 (https://fantom.gsc.riken.jp/5/):

    FANTOM5 is atlases of mammalian promoters, enhancers, lncRNAs and miRNAs in human, mouse, rat, dog, chicken, and rhesus monkey.

  8. PsychEncode (http://resource.psychencode.org/):
    An integration of data across the capstone projects to build a model taking QTLs as inputs and providing both phenotype predictions as well as functional modules involved.

QTLs/Interactions

  1. GTEx (https://gtexportal.org/home/):

    WGS, WES, and RNA-seq data were measured in 54 non-diseased tissue across ~1,000 individuals; snRNA-seq data released (7/20/2021), 8 tissues in 16 donors

  2. DICE (https://dice-database.org/):

    Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types.

  3. eQTL Catalogue (https://www.ebi.ac.uk/eqtl/):

    A resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 112 datasets across 21 studies including BLUEPRINT, TwinsUK, BrainSeq, ROSMAP, GTEx (v8), etc.

  4. QTLbase (http://mulinlab.org/qtlbase):
    QTLbase curates and compiles genome-wide QTL summary statistics for many human molecular traits across over 70 tissue/cell types.

  5. 3DIV (http://www.3div.kr/capture_hic):
    Maps of long-range chromatin interactions centered on 18,943 known promoters for protein-coding genes in 27 cell/tissue types