The process is repeated for all LD proxies. The highest scoring LD proxy is used to determine the overall score of the original SNP, rs3762611, provided the score of the proxy is greater than the score of the original. In this case, the LD proxy rs16859826 was used to determine the overall score of rs3762611. This computation takes into account the strength of the LD proxy, so that proxies with smaller values of r2 have smaller scores and are less likely to be used. Also, a fixed penalty is applied to the score of the proxy in order to ensure LD proxies are only used when they have better scores than the original, even when r2 = 1. The default LD penalty of 0.9 is moderate so that LD proxies will be given significant attention when prioritizing SNPs. This parameter can be configured on SPOT’s main page.
