Chunk #51 — Materials and Methods — Enrichment analysis of trait-associated SNPs and SNPs located within the HLA region

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Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.

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To assess enrichment of trait-associated SNPs, we used a collection of 1,262 unique SNPs from 'A Catalog of Published Genome-Wide Association Studies' (accessed 09 February 2010, and each having at least one reported association p-value <5.0×10−7). We could successfully impute the genotypes for 1,167 of these SNPs and therefore confined all analyses to these SNPs. Of these SNPs 572 had been directly genotyped on the Illumina HumanHap300 platform, with a MAF>0.05, an HWE exact p-value >0.0001 and call-rate >95%.