Protocol

Retrieving HapMap Data Using HapMart

This protocol was adapted from "Using the HapMap Web Site," Chapter 6, in Genetic Variation (eds. Weiner et al.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2007.

INTRODUCTION

The primary goal of the International Haplotype Map Project has been to develop a haplotype map of the human genome that describes the common patterns of genetic variation, in order to accelerate the search for the genetic causes of human disease. Within the project, ~3.9 million distinct single-nucleotide polymorphisms (SNPs) have been genotyped in 270 individuals from four worldwide populations. The project data are available for unrestricted public use at the HapMap Web site. This site, which is the primary portal to genotype data produced by the project, offers bulk downloads of the data set, as well as interactive data browsing and analysis tools that are not available elsewhere. Because of performance considerations, interactive access to HapMap data via the genome browser on the HapMap Web site is limited to regions no more than 5 Mb wide. Researchers who wish to obtain data for chromosome- or genome-wide data have two choices: Bulk download or HapMart access. HapMart, described in this protocol, allows researchers to select SNPs using diverse criteria and to display just those aspects of the data set that they are interested in.