The main panel of a LocusZoom plot shows association P-values on the −log10 scale on the vertical axis, and the chromosomal position along the horizontal axis (Fig. 1). The user can specify the region to display in one of three ways: (i) an index SNP and a window size, (ii) the chromosome together with start and stop positions or (iii) gene name and size of flanking region. We allow for the display of a ‘rug’ above the main panel which gives a tick for any SNP in the results file, or for all SNPs from HapMap Phase II. The plots were designed to display ∼1 Mb windows of the genome, although for regions with several association signals or long-range LD patterns, plots extending further can be drawn.
