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. 2018 May 17;8:7806. doi: 10.1038/s41598-018-26112-1

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Visualization of two replicated 3-SNP haplotype logic trees containing SNPs in the HLA region. The plotted region spans chr6:32156782–32585905 (hg19), which corresponds with the red rectangle in the chromosomal ideogram. The top data track shows single-SNP association results and haplotype association results using benchmark (“3-SNP sliding window”) and proposed (“3-SNP logic tree”) methods for the selected genomic region. The subsequent annotation tracks show RefSeq genes, a heatmap corresponding to Roadmap Epigenomics²¹ H3K4me1 (Enh) and H3K4me3 (TSS) ChIP-seq peaks in primary B cells (E032) and primary T cells (E034), and the top significant blood (BLD), lymphoblastoid (LCL), and liver (LIV) eQTLs (expression quantitative trait loci) associated with SNPs in replicated haplotypes (GTEx Consortium)²⁰.