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. 2012 Nov 15;41(Database issue):D64–D69. doi: 10.1093/nar/gks1048

Figure 2.

Figure 2.

Genome Browser image of the promoter region and transcription start of IRF1 on human assembly hg19 showing UCSC Genes, 1000 Genomes Phase 1 Integrated Variant Calls in the haplotype sorting VCF display mode, histone mark H3K27Ac binding in overlays of 7 ENCODE cell lines and PhyloP conservation scores from alignments of placental mammals. Mouse-over text gives the dbSNP identifier and genotype counts for one of the 1000 Genomes variants. The variant outlined in purple is used as the center variant for clustering haplotypes by similarity, and is clearly in linkage with nearby variants. Wider purple triangular leaves of the clustering tree indicate more common local haplotypes. Note that the reference genome haplotype (horizontal run of invisible reference alleles) is often not the major haplotype among the 1000 Genomes Phase 1 samples.