Finding a SNP
Very similar to the questions we asked when finding a gene, it is often important to assess association for individuals SNPs. Furthermore, if such SNPs are not present in the WGA dataset, it would then be important to know whether there are LD proxies for these SNPs, and what are their P values.
We take the pre-annotation dataset “CHAVI_SETPOINT_SCIENCE. wr” as an example. Suppose we would like to know about the results for an interesting SNP rs1573649, which is a nonsynonymous coding SNP located on exon 1 of HLA-DQB2 gene. Clicking on menu “ Tools->Find a SNP ” will activate a dialog for annotation parameters (Figure 3.5-1). In this example we use the HapMap database to search for the LD proxies. The LD search span is the region around the target SNP that will be checked for proxies. This process will then lead to an annotation result as shown in Figure 3.5-2, where it is explicitly shown that not only the target SNP itself (rs1573649), but also its proxies (for example, rs2301271, r2=0.817) were genotyped in the WGA project, and none are significantly associated with the set point phenotype.
One has the option to search for the LD proxies using pre-calculated LD dataset by Haploview or PLINK, instead of using the HapMap data. There is also an option to search for specific SNPs only, not including their LD proxies (Figure 3.5-1). Both of these two options do not require an internet access.
Figure 3.5-1. Parameters for finding a SNP.
Figure 3.5-2. Finding a SNP: annotation results. (Click to enlarge)