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HapMap, a database and analysis resource of human variation

Tutorial and training materials by OpenHelix

Learn to use HapMap, a database and analysis resource of human variation. The HapMap project identified and cataloged genetic variation in human beings in four populations with African, Asian, and European ancestry. This freely available database and variation browser contains much of the known variation of the Human genome and researchers can use the data to determine variations that affect health, disease, and individual responses to medications and environmental factors. Learn to use the genome browser associated with this project to view HapMap data, retrieve genotypes and find frequencies for genomic regions.
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You'll learn:

  • to find SNPs of interest with advanced searching
  • how to determine linkage disequilibrium between SNPs
  • how to find candidate tag SNPs to better design genotyping assays
  • where to download and how to use the HaploView software for deeper SNP analysis


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Recent BioMed Central research articles citing this resource

Smith K Alicia et al., Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-145

Zhang Hongmei et al., The interplay of DNA methylation over time with Th2 pathway genetic variants on asthma risk and temporal asthma transition. Clinical Epigenetics (2014) doi:10.1186/1868-7083-6-8

Pardo-Seco Jacobo et al., Evaluating the accuracy of AIM panels at quantifying genome ancestry Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-543

Greminger P Maja et al., Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms Non-human and non-rodent vertebrate genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-16

Choudhury Ananyo et al., Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-437

More about the resource:

The International HapMap Project is a collaborative international effort of over 24 groups in six countries to identify and catalog human variation. The project has cataloged most of the probably 10 million SNPs estimated to occur in the Human Genome. The HapMap website includes a browser to view the SNP, haplotype, linkage disequilibrium and tag SNP data, an advanced search tool and software for deeper analysis. All data and tools are free and in the public domain.


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Copyright 2009, OpenHelix, LLC.

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