We explored whether integration of the location of tissue-specific regulatory and coding DNA regions could increase resolution in statistical fine-mapping. The ENCODE [18] project provided a wealth of genomic landmarks that were systematically integrated to segment the genome into seven major classes: transcription start site and predicted promotor region (TSS) (1.2%), predicted promotor flanking region (PF) (0.7%) predicted enhancer (E) (1.8%) predicted weak enhancer (WE) (2.5%), CTCF-enriched element (CTCF) (0.1%) predicted transcribed region (T) (19.3%) and finally, predicted repressed or low-activity region (R) (69.6%). We examined these genomic segmentations for the six primary ENCODE cell lines: gm12878 (lymphoblastoid), h1hesc (embryonic stem cells), helas3 (cervical cancer), hepg2 (liver carcinoma), huvec(umbilical vein endothelial cells), and k562 (chronic myelogenous leukemia). In addition, we also explored 403 broadly defined (peak 1 Kb) DNase I Hypersensitivity Sites spanning numerous tissues and cell lines. Of these 403 DHS I maps, 349 came from Maurano et al. [19], 73 DHS I annotations from Thurman et al. [42], with the remaining DHS annotation being an overall DHS map derived from UCSC genome browser. These annotations have been used recently in the context of GWAS [10].
