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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 be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

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 (refSNP ID(s), comma-delimited):
or, upload a text file (one refSNP ID per line):
or, select a GWAS:

Set Options

Genome version: hg18hg19
LD threshold, r² (select NA to only show query variants):
1000G pilot population for LD calculation: ASN (CHB+JPT) CEU YRI
Browse ENCODE: Off On (Please see notes)
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:
Background set for enhancer enrichment analysis:


For usage examples, click here (opens in a pop-up window.)

For details on data sources and methods, see the full documentation (opens in a new window.)

The HaploReg database and web interface were produced by Luke Ward in collaboration with the Computational Biology Group at MIT. HaploReg is hosted by the Broad Institute.

To cite HaploReg, please refer to our 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).

Contact: lukeward@mit.edu.