In the following runs of SPOT, the default LD settings were used so that LD proxies from the HapMap CEU (European–American) sample are used with a threshold of r2 ≥ 0.8. The default setting of a maximum of 1000 SNPs limits the number of SNPs sent to the output tables, but does not limit SNPs used as input, and the P-value threshold is set to 0.05 so that only SNPs with P ≤ 0.05 are used in the GIN model. The example data provided on the main page (10 SNPs and 4 queries retrieving 10 genes) took 3 s to run, and a more typical run of 1 million SNPs with randomly selected, and therefore uniformly distributed, P-values and 1000 prioritized genes took 57 s (in this case, about 50 000 SNPs were used for prioritization given the P ≤ 0.05 filter). A more ambitious run of 1 million SNPs and 10 000 prioritized genes took 3 min and 13 s.
