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. 2012 Apr 11;7(4):e35333. doi: 10.1371/journal.pone.0035333

Figure 2. Regional linkage disequilibrium (LD) near the CYP27A1 locus on chromosome 2.

Figure 2

Top: the position of GWAS SNPs and RefSeq genes located within the regional LD block are drawn. On the X-axis, genomic position in kb, aligned to NCBI genome build 36 coordinates. On the left Y-axis, −log10(p values) for the strongest cis 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 (RQCD1), 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 Y-axis, −log10(p values) from the replication GWAS analysis for SNPs within the region (black line), SNPs modulating CYP27A1 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 [50], using the standard D'/LOD color scheme.