Figure 1 shows a screenshot from SPOT displaying the GIN diagram for the SNP rs3762611, which is in the example data provided on SPOT’s main page. The diagram, created dynamically by SPOT using GraphViz (http://www.graphviz.org), shows how the overall GIN prioritization score was determined for rs3762611. When determining the score, SPOT takes into account all possible LD proxies—SNPs with r2 above a certain threshold in a specific HapMap (6) sample. We used genotype data from HapMap Public Release 27 (http://hapmap.ncbi.nlm.nih.gov) and the program Haploview (7) to estimate the r2 LD coefficients in each of the 11 populations from this release. Figure 1 shows the GIN calculations for the LD proxy rs16859826, which was determined using the HapMap European American sample. The overall prioritization score is computed by traversing the network diagram from left to right and adding up scores from the different nodes as described in (4). SNPs with higher biological relevance, such as those in genes, particularly user-specified priority genes, and in conserved regions, receive higher scores.
