Top hits: Chromosome view (Figure 3.3.2.a-1)

Click on the “Chromosome” tab to display the chromosome view panel (Figure 3.3.2.a-1). This panel shows the SNP and P values spanning the annotation window around the annotated top hit, that is, as shown from Figure 3.3.2.a-1, 200Kbp upstream and downstream to rs9264942. Each P value line responds to mouse movement and a small stick with SNP rs number and P value will appear over the targeted SNP. The chromosome ideogram also shows the approximate position of the annotated region with a transparent red rectangle. All the P value lines plotted in this panel are spaced evenly. If the whole panel cannot accommodate all the P value lines, the program will automatically determine a resolution and displays only the lowest P value for the adjacent n SNPs. The resolution will be shown on the right upper corner: “Current resolution”.

Figure 3.3.2.a-1. Results of comprehensive annotation for top hits: rs9264942, chromosome view. (Click to enlarge)

Next: Top hits annotation: gene view; SNP view