PT - JOURNAL ARTICLE AU - Hilary K. Finucane AU - Brendan Bulik-Sullivan AU - Alexander Gusev AU - Gosia Trynka AU - Yakir Reshef AU - Po-Ru Loh AU - Verneri Anttilla AU - Han Xu AU - Chongzhi Zang AU - Kyle Farh AU - Stephan Ripke AU - Felix Day AU - ReproGen Consortium AU - Schizophrenia Working Group of the Psychiatric Genetics Consortium AU - The RACI Consortium AU - Shaun Purcell AU - Eli Stahl AU - Sara Lindstrom AU - John R.B. Perry AU - Yukinori Okada AU - Soumya Raychaudhuri AU - Mark Daly AU - Nick Patterson AU - Benjamin M. Neale AU - Alkes L. Price TI - Partitioning heritability by functional category using GWAS summary statistics AID - 10.1101/014241 DP - 2015 Jan 01 TA - bioRxiv PG - 014241 4099 - http://biorxiv.org/content/early/2015/01/23/014241.short 4100 - http://biorxiv.org/content/early/2015/01/23/014241.full AB - Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here, we analyze a broad set of functional elements, including cell-type-specific elements, to estimate their polygenic contributions to heritability in genome-wide association studies (GWAS) of 17 complex diseases and traits spanning a total of 1.3 million phenotype measurements. To enable this analysis, we introduce a new method for partitioning heritability from GWAS summary statistics while controlling for linked markers. This new method is computationally tractable at very large sample sizes, and leverages genome-wide information. Our results include a large enrichment of heritability in conserved regions across many traits; a very large immunological disease-specific enrichment of heritability in FANTOM5 enhancers; and many cell-type-specific enrichments including significant enrichment of central nervous system cell types in body mass index, age at menarche, educational attainment, and smoking behavior. These results demonstrate that GWAS can aid in understanding the biological basis of disease and provide direction for functional follow-up.