The NIH NHGRI catalog of published genome-wide association studies29 (GWAS catalog, downloaded May 7, 2012) contained 7,899 SNP-disease/trait associations. We extended this set to 190,356 autosomal associations by propagating disease/trait associations to proxy SNPs using the SNAP proxy search tool70 (http://www.broadinstitute.org/mpg/snap/) based on linkage disequilibrium (r2 > 0.8) between SNPs (within 250kb) in any of the three populations in the 1000 genomes project pilot71 data. The 1000 genome data coordinates were in hg18 coordinates and were mapped to hg19 using the UCSC liftOver tool72.
