Annotation for a SNP
The function of this tool is very similar to the SNP annotation procedures in WGAViewer, except that no WGA results are involved.
Click on menu “Tools -> Annotate a SNP”. Setup the annotation parameters, for example, as in Figure 3.11.2-1, to annotate SNP rs9264942 with an up- and down-stream span of 100kbp, and a genotype-expression association test with gene HLA-C. One has the option to use HapMap data for LD calculation, or use pre-calculated LD dataset by PLINK or Haploview. This will result in a typical SNP annotation as discussed in this user guide (see: section 3.3.2.c, Figure 3.3.2.c-1), however with no WGA results involved (Figure 3.11.2-2).
Figure 3.11.2-1. Tools: Annotation for a SNP. (Click to enlarge)
Figure 3.11.2-2. Tools: Annotation for a SNP: results. (Click to enlarge)