Regional linkage disequilibrium (LD) near the <i>CYP27A1</i> locus on chromosome 2.

<p>Top: the position of GWAS SNPs and RefSeq genes located within the regional LD block are drawn. On the <i>X</i>-axis, genomic position in kb, aligned to NCBI genome build 36 coordinates. On the left <i>Y</i>-axis, −log₁₀(p values) for the strongest <i>cis</i> eQTL association for a gene in the replication data, the vertical position of genes (drawn as arrows) are aligned to this axis and thus represent statistical significance. For one gene (<i>RQCD1</i>), no SNP-transcript pair and, therefore, no eQTL p value was available in our data. This gene is shown as a dashed arrow. On the right <i>Y</i>-axis, −log₁₀(p values) from the replication GWAS analysis for SNPs within the region (black line), SNPs modulating <i>CYP27A1</i> expression are shown as black dots, other SNPs are grey. Bottom: pairwise linkage disequilibrium for HapMap phase III release 2 SNPs (CEU+TSI populations). The LD plot was created in Haploview v4.2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035333#pone.0035333-Barrett2" target="_blank">[50]</a>, using the standard <i>D'</i>/LOD color scheme.