We have extended the protein-coding genes detail pages in the UCSC Genes track on the GRCh37/hg19 human assembly to include a section that displays and compares ‘gene haplotype alleles’ generated from phased chromosomal data from Phase 1 of the 1000 Genomes Project (19) (Figure 1). Each haplotype allele is a distinct set of variants found on at least one of the 1000 Genomes subject chromosomes. By default the common non-synonymous variants (those of at least 1% frequency) are displayed, although rare haplotypes are optionally available. The Browser shows the frequency of each haplotype in the 1000 Genomes populations and indicates the frequency with which it occurs homozygously. Unexpected frequencies of occurrence may be used to identify alleles that merit further study. Predicted protein sequence for common haplotypes can also be displayed, allowing differences among alleles to be used to identify differences at the amino acid level. To access the gene haplotype alleles information, go to the details page for any protein-coding gene in the UCSC Genes track (GRCh37/hg19 assembly) and click the ‘Gene Alleles’ link in the ‘Page Index’ matrix. For more information, see http://genome.ucsc.edu/goldenPath/help/haplotypes.html.
