TY - JOUR T1 - GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction JF - bioRxiv DO - 10.1101/085738 SP - 085738 AU - Valentina Iotchkova AU - Graham R.S. Ritchie AU - Matthias Geihs AU - Sandro Morganella AU - Josine L. Min AU - Klaudia Walter AU - Nicholas Timpson AU - UK10K Consortium AU - Ian Dunham AU - Ewan Birney AU - Nicole Soranzo Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/07/085738.abstract N2 - Loci discovered by genome-wide association studies (GWAS) predominantly map outside protein-coding genes. The interpretation of functional consequences of non-coding variants can be greatly enhanced by catalogs of regulatory genomic regions in cell lines and primary tissues. However, robust and readily applicable methods are still lacking to systematically evaluate the contribution of these regions to genetic variation implicated in diseases or quantitative traits. Here we propose a novel approach that leverages GWAS findings with regulatory or functional annotations to classify features relevant to a phenotype of interest. Within our framework, we account for major sources of confounding that current methods do not offer. We further assess enrichment statistics for 27 GWAS traits within regulatory regions from the ENCODE and Roadmap projects. We characterise unique enrichment patterns for traits and annotations, driving novel biological insights. The method is implemented in standalone software and R package to facilitate its application by the research community. ER -