All variants passing quality control (QC) were annotated to examine if variants overlapped with bioinformatic features from the following databases: UCSC Genome Browser and GENCODE (for a full list of annotations see Table S1). To determine their novelty, identified variants were compared with dbSNP v141 (Phillips, 2007) and the 1000 Genomes Database (Clarke et al., 2012) (1KG). Variants were also annotated for overlap with 15 chromatin states, elements that regulate gene transcription (Baker, 2011), in liver and brain tissue from the anterior caudate, hippocampus, mid-frontal lobe, and substantia nigra regions, which are all known to be involved with alcohol addiction (Ozsoy et al., 2013, Wrase et al., 2008, Bassareo et al., 2003, George et al., 2001). See Supplemental Material for a description of the chromatin states and how they were generated by the Roadmap Epigenomics Project (Kundaje et al., 2015).
