Many of you will be familiar with the data in the GWAS catalog which contains typically the top SNP and P value for each locus and trait. However, there are often a number of SNPs in supplementary tables that have other SNPs that were either not the best P value and in LD or did not meet GWAS thresholds. A number of these have been culled from supplementary tables and other sources. Two that I know of are that of the those done by the Wang lab located here and another by Johnson and O'Donnell which can be downloaded here. (Original papers for these are here and here.)
My question is two-fold: 1. Are these the best sources or are there others which have culled P values for GWAS traits from papers? 2. If we haven't genotyped one of the SNPs from these catalogs and we wanted to pick surrogates in high LD that were genotyped, what might be the best means by which to select such SNPs?
The Venn diagram here showing the 829+158 ungenotyped SNPs may best illustrate our problem.