The association between non-coding variants and human diseases has been of an increasing concern, and variants that are associated with gene expression abundance have been rapidly identified and accumulated in recent years. Annotating the regulatory features of human variants has been a practical requirement in clinical and basic research; multiple approaches have been developed to allow the functional annotation of non-coding variants.
Creates a large references panel of human haplotypes by combining together sequencing data from multiple cohorts. HRC is a reference panel of 64 976 human haplotypes at 39 235 157 single nucleotide polymorphisms (SNPs) constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Ultimately, HRC is a single centralized resource for human genetic researchers to carry out genotype imputation.
Serves for linking human noncoding single nucleotide polymorphisms (SNPs) to their three-dimensional interacting genes. 3DSNP is an online repository that annotates the regulatory function of human noncoding SNPs. Moreover, this resource integrates sequential and genotyping data, 3D chromatin interactions, phenotyping data and a variety of chromatin signatures across a broad range of cell types.
Classifies, queries and annotates genomic variation of all sizes. Seave supports variant types including single nucleotide variants (SNVs), Indels, copy number variants (CNVs), structural variants (SVs) and regions of homozygosity (ROH). It allows familial filtering on standard inheritance patterns using any combination of family members. This platform offers functions to edit the family structure to handle individuals with uncertain phenotype.
Collects and annotates single nucleotide polymorphism (SNPs) with known and predicted regulatory elements in the intergenic regions of human genome. RegulomeDB integrates all available ENCORE transcription factor (TF) ChIP-seq, FAIRE, DNase I hypersensitive site data from the Project Consortium 2012 and TF ChIP-seq from the NCBI Sequence Read Archive. In total, this repository gathers more than 900 experimental data sets that cover over 100 tissues and cell lines and representing nearly 60 million of annotations.
Compiles results from a framework based on a predictive model for four epigenetic assays. DeepFIGV relies DNA sequence to quantitative variation in epigenetic signal and evaluates the predicted functional impact of genetic variants on multiple assays. This repository can be used to understand the molecular mechanism of a causal variant and prioritize downstream experiments or, in conjunction with large-scale genome-wide association studies.
Offers access to primary experimental data, well-documented data collection protocols and analysis tools. MPD contains a broad scope of behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. This database contains more than 1 227 000 individual animal data points and 60 million single nucleotide polymorphism (SNP) genomic locations.