HaploReg v5

 MIT Computational Biology
Broad Institute

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. Version 5 rebuilds the annotation pipeline on the 1000 Genomes high-coverage call set (GRCh38), with linked SNPs and small indels shown alongside ChromHMM chromatin states across reference epigenomes, regulatory motif alterations scanned with MOODS, sequence constraint, GWAS associations and eQTLs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Update 2026.10.28: Version 5.0 (Classic) keeps the familiar v4 interface on top of the new v5 data layer. Positions are reported in hg38 and allele frequencies for all five 1000 Genomes superpopulations (AFR, AMR, EAS, EUR, SAS). Until the v5 pipeline backend is online, the default data source is the live Ensembl REST API; an offline demo source with synthetic chromatin annotations is available under Set Options.

Update 2026.10.28: Try the redesigned interface, HaploReg Explore. Older versions available: v4.2.

Build Query

Use one of the three methods below to enter a set of variants. If an r² threshold is specified (see the Set Options tab), results for each variant will be shown in a separate table along with other variants in LD. If r² is set to NA, only queried variants will be shown, together in one table.

Query (comma-delimited list of rsIDs OR a single region as chrN:start-end):
or, upload a text file (one refSNP ID per line):
or, select a GWAS:

Set Options

LD threshold, r² (select NA to only show query variants):
1000G population for LD calculation:
Source for epigenomes:
Mammalian conservation algorithm: GERP SiPhy-omega both
Show position relative to: GENCODE genes RefSeq genes both
Condense lists in table longer than:
Condense indel oligos longer than:
Output mode: HTML Text
Data source:

Documentation

For definitions of every column, option and term, data sources, the chromatin-state color key and usage examples, see the full documentation (opens in a pop-up window). Throughout the interface, click a ? to jump straight to the definition of the item next to it.

Enter one or more rsIDs (for example rs7903146), a region such as chr10:112990000-113000000, upload a file of rsIDs, or choose a curated GWAS locus set. Each query variant is expanded to all variants in linkage disequilibrium above the chosen r² threshold in the selected superpopulation, and every variant is annotated. Click a variant to open its detail view.

Columns. Promoter and enhancer histone marks summarize the epigenomes in which the variant falls in a promoter- or enhancer-associated chromatin state (or histone peak, depending on the epigenome source); hover over a cell to list the epigenomes. Lists longer than the condense setting are replaced by counts of distinct tissues. Motifs changed lists position weight matrices whose match score changes between the reference and alternate allele.

Data sources. Live — Ensembl REST returns real hg38 positions, 1000 Genomes Phase 3 frequencies and LD, NHGRI-EBI GWAS hits, VEP consequences and GERP scores, and Ensembl Regulatory Build overlaps; per-epigenome chromatin states and eQTLs require the v5 pipeline backend. Demo works offline with synthetic annotations for interface development only.

The HaploReg database and web interface were originally produced by Luke Ward in the Kellis Lab at MIT. To cite HaploReg, please refer to the publication in Nucleic Acids Research: HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants (PMID:22064851).

The HaploReg v5 web interfaces, this Classic view included, were built by Pranava Kumar.

Contact: haploreg@mit.edu