Identification of functional variants is an end-game of analysis of genetically influenced diseases and starting point to understand roles of genes. Addictions are moderately to highly heritable but most of the genetic variance is unexplained by functional loci or replicated linkages. Using genomic approaches and focused studies on implicated genes, we have discovered several functional loci with roles in complex behaviors relevant to alcohol use disorders (AUD) and other addictions. These studies make use of founder populations, people at risk due to exposures, and model organisms. We use intermediate phenotypes that are closer to gene action. Model organisms, including artificially selected mice, rats and fruitflies are used for gene discovery, as well as validation and we use cellular models including iPSC's to bridge between animal models and humans. An OPRM1 Asn40Asp missense variant (Bergen et al, 1997) was found to be functional and linked to naltrexone treatment response in AUD(Anton et al, 2008). A common, functional SNP in the serotonin transporter HTTLPR (Hu et al, 2007) enhanced linkage to OCD,neuroimaging responses to emotion, and gene x stress interactions leading to suicidality (Roy et al, 2007). Common HTR2C Ser23Cys (Lappalainen et al, 1999, Okada et al, 2004) and HTR2A Asn452His variants(Ozaki et al, 1997) were found, shown to be functional, and linked to behavior, including clozapine response. In first-episode schizophrenics, we found that a functional DRD2 promoter variant influences antipsychotic response (Lencz et al, 2006). We traced linkages of functional loci and haplotypes of NPY (Zhu et al, 2008), GCH1 (Tegeder et al, 2006) and DISC1 (Hodgkinson et al, 2004) to emotionality, schizophrenia and pain. By deep sequencing we found an HTR2B stop codon that is relatively common in Finns, a founder population, absent in others, and associated with but not determinant for impulsive behavior. This stop codon cosegregated with ASPD and AUD in families and the mouse gene knockout was impulsive and high in novelty seeking and novelty response. It leads to variable nonsense mediated decay of the HTR2B RNA and blocked HT2B receptor expression (Bevilacqua et al, Nature, 2010). A low expression Neuropeptide Y (NPY) haplotype increased anxiety and emotionality but had stronger effects on molecules (NPY RNA and protein) and intermediate phenotypes (brain imaging responses to emotion and pain/stress)(Zhou et al, Nature, 2008). Because intermediate phenotypes augment analysis of behavior (Ducci and Goldman)we proposed a multidimensional Addictions Neuroclinical Assessment based on the addiction cycle (Kwako et al, Biol Psych, 2016). The imaging genetics paradigm we helped initiate (Heinz et al, 2000; Hariri et al, 2002; Egan et al, 2001; 2003; Zubieta et al, 2003) led to groundbreaking findings. We found a mechanism of CHRNA5 Asn398, a functional locus altering nicotine addiction risk. The risk allele weakens brain connectivities including a Dorsal Anterior Cingulate/Ventral Striatal circuit predictive of craving (Hong et al, 2010). Clinical subphenotyping enabled linkage of HTR1B to antisocial alcoholism (Lappalainen et al, 1998), serotonin transporter (SLCA4) to anxiety (Mazzanti et al; Hariri et al), BDNF Val66Met to episodic memory (Egan et al, cell, 2003), and GTP cyclohydrolase to chronic pain and experimental pain response (Tegeder et al, 2006). Frontal cognitive deficit is a risk factor in schizophrenia, alcoholism and other diseases. Dopamine generally enhances prefrontal cortical efficiency. Met158, a common COMT variant, leads to four-fold reduction in COMT activity. It is thus a candidate allele for cognitive function via effect on frontal dopamine. We found an allele-dosage relationship of Met158 to frontal cognitive function and diminished cortical efficiency (Egan et al, 2001). The effect on cognition is seen in populations differing in baseline cognitive function: schizophrenia, head injury (Lipsky et al, 2005, 2011), & controls (Malhotra et al, 2002, 2009). We proposed that Val158 has a counter-advantage: stress resiliency. In two populations Met158 predicted anxiety in women and decreased frontal EEG coherence (Enoch et al, 2003), and Met158 was associated with lower resiliency to pain/stress (Zubieta et al, Science, 2003; Diatchenko et al, 2005, 2006). We have extended knowledge of GxE effects of stress related genes such as COMT, NPY, SLC6A4 and SLC6A4 in many studies using both behavioral and endocrine outcomes (Lovallo et al 2015, 2016). A functional polymorphism of Fatty Acid Amide Hydrolase (FAAH) which metabolizes the endogenous ligand for cannabinoid receptors, specifically predicts placebo response to pain (Pecina et al, 2014). GWAS, transcriptomics and exome sequencing are global approaches that enable the genomic space to be searched independent of prior hypotheses. Via transcriptomics we have recently advanced understanding of glia in addictions (De Biase, 2017), developmental effects of nicotine (Jung, 2016), and found an intrinsic cellular difference in women with Premenstrual Dysphoric Disorder (Dubey,2016). The Chr 4 GABAA genecluster was implicated in alcoholism by family linkage (Long et al, 1998), an effect that appears anxiety-modulated (Enoch et al, 2006). Another GABAA gene cluster implicated in alcoholism and alcohol response is located on Chr 5 (Radel et al, 2005). GABRA6 has a missense variant associated with alcohol dependence and response to alcohol and diazepam (Iwata et al, 2005). A family linkage scan yielded genome-wide significant linkage of CRH-BP to an alcoholism-associated EEG trait and this was supported by association in two populations (Enoch et al, 2008). GWAS of EEG (Hodgkinson et al, PNAS, 2010) in Plains Indians detected three independent genome-wide significant loci(Hodgkinson et al, PNAS 2010). Via GWAS, a schizophrenia risk locus was identified in multiple populations (Lencz et al, Nat Commun, 2013). Founder, phenotypically extreme, and exposed populations enhance power to detect gene effects. Our Finnish dataset, derived from a founder population, was ascertained via criminal alcoholic probands. SW and Plains Indian samples represent founder populations. An African American substance dependence sample with high adversity revealed GxE of childhood trauma and HTTLPR in suicidality (Roy et al, 2007). Stress and poverty, but not African ancestry, predicted high risk of addictions (Ducci et al, 2009). An MAOA VNTR previously linked to dyscontrol via stress interaction was linked to outcomes of alcohol dependence and ASPD in American Indian women, of whom half had been sexually abused as children (Ducci et al, 2008). A strong interaction between a MAOA VNTR and testosterone was observed in the Finnish criminal sample (Sjoberg et al, 2008). As mentioned, deep sequencing in Finns detected a population-specific HTR2B Stop codon significant for impulsivity (Bevilacqua et al, Nature, 2010). We exome-sequenced an artificially selected animal model for alcoholism, the P/NP rat, and discovered a stop codon in the metabotropic glutamate receptor 2 (Grm2) gene that leads to altered glutamate function and increased alcohol preference in alcohol-preferring rats (Zhou et al, 2013). The Grm2 Stop codon is common (0.08) in parental Charles River Wistar rats, and fixed in Wistar from some sources. It leads to uncompensated changes in glutamate function. It was genetically fixed by artificial selection in the alcohol preferring and non-preferring rats illustrating the power of using such strains to discover alleles that alter behavior. Via parallel exome sequencing in selected strains and people we are identifying genes involved in drug reward and withdrawal. As facilitated by a NIDA RFA leading to two U01 grants we have identified new loci altering addiction in rat and Drosophila.