Genome-wide association study implicates CHRNA2 in cannabis use disorder


Cannabis is the most frequently used illicit psychoactive substance worldwide; around one in ten users become dependent. The risk for cannabis use disorder (CUD) has a strong genetic component, with twin heritability estimates ranging from 51 to 70%. Here we performed a genome-wide association study of CUD in 2,387 cases and 48,985 controls, followed by replication in 5,501 cases and 301,041 controls. We report a genome-wide significant risk locus for CUD (P = 9.31 × 10−12) that replicates in an independent population (Preplication = 3.27 × 10−3, Pmeta-analysis = 9.09 × 10−12). The index variant (rs56372821) is a strong expression quantitative trait locus for cholinergic receptor nicotinic α2 subunit (CHRNA2); analyses of the genetically regulated gene expression identified a significant association of CHRNA2 expression with CUD in brain tissue. At the polygenic level, analyses revealed a significant decrease in the risk of CUD with increased load of variants associated with cognitive performance. The results provide biological insights and inform on the genetic architecture of CUD.

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Fig. 1: CUD GWAS results.
Fig. 2: Association results for the genomic region with the CUD risk locus.
Fig. 3: Association of CHRNA2 expression with CUD.
Fig. 4: Association of PRS with CUD.

Data availability

Summary statistics with the results from the CUD GWAS are available on the iPSYCH website ( For access to the genotypes from the iPSYCH cohort, interested researchers should contact A.D.B.


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The iPSYCH project is funded by the Lundbeck Foundation (grant nos. R102-A9118 and R155-2014-1724) and the universities and university hospitals of Aarhus and Copenhagen. Genotyping of the iPSYCH samples was supported by grants from the Lundbeck, Stanley and Simons Foundations (grant no. SFARI 311789 to M.J.D.), and the National Institute of Mental Health (NIMH; grant no. 5U01MH094432-02 to M.J.D.). The study was supported by a European Commission Horizon 2020 Programme grant no. 667302 (CoCA) to A.D.B. The Danish National Biobank resource was supported by the Novo Nordisk Foundation. Data handling and analysis on the GenomeDK HPC facility was supported by the NIMH (grant no. 1U01MH109514-01 to M. O’Donovan and A.D.B.). High-performance computer capacity for the handling and statistical analysis of the iPSYCH data on the GenomeDK HPC facility was provided by the Centre for Integrative Sequencing (iSEQ) at Aarhus University, Denmark (grant to A.D.B.). Work at deCODE was supported in part by the National Institute of Health (R01DA034076). We gratefully acknowledge all the studies and databases that made the GWAS summary data available: Genetics of Personality Consortium, Psychiatric Genomics Consortium, Social Science Genetics Association Consortium (SSGAC), Tobacco and Genetics Consortium, UK Biobank and Complex Traits Genetics Lab. We gratefully acknowledge the data made available by the GTEx Project (supported by the Common Fund of the Office of the Director of the National Institutes of Health, National Cancer Institute, National Human Genome Research Institute, National Heart, Lung, and Blood Institute, National Institute on Drug Abuse, NIMH and National Institute of Neurological Disorders and Stroke). The data used for the analyses described in this manuscript were obtained from on 1 November 2017.

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D.D. and A.D.B. conceived the idea, and supervised and directed the study. T.E.T., T.T., V.R., J.B.-G., M.B.-H., A.T., E.A., D.M.H., T.W., O.M., P.B.M., M. Nordentoft, M.J.D., H.S., K.S. and A.D.B. provided samples and/or data. D.D., V.M.R., T.E.T., T.D.A., J.G., K.L., D.F.G., J.P., G.W.R., L.M.H. and E.A.S. performed the analyses. D.D., V.M.R., T.E.T., T.D.A, J.G., K.L., D.F.G., P.Q., C.H., J.H.C., H.S., M. Nyegaard and A.D.B. interpreted the results. D.D. wrote the manuscript. The core revision group consisted of D.D., T.E.T., J.G., K.L., D.F.G., H.S. and A.D.B. All authors discussed the results and approved the final version of the manuscript.

Corresponding authors

Correspondence to Ditte Demontis or Anders D. Børglum.

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Competing interests

T. Werge has been a lecturer and advisor to H. Lundbeck A/S. T.E. Thorgeirsson, D.F. Gudbjartsson, G.W. Reginsson, H. Stefansson and K. Stefansson are employees of deCODE genetics/Amgen.

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Integrated supplementary information

Supplementary Fig. 1 Null distribution for rs56372821 odds ratio for schizophrenia.

Null distribution of the odds ratio for rs56372821 when applying 10,000 permutations removing randomly 554 schizophrenia cases and 101 individuals. The Red lines indicate the observed ln(ORrs56372821) when excluding individuals with CUD (554 SZ cases and 101 controls with CUD) mirrored around the mean ln(ORrs56372821) of the null distribution obtained by random removal of the same number of SZ cases and control.

Supplementary Fig. 2 CHRNA2 expression in cerebellum among rs56372821 genotypes.

The distribution of CHRNA2 expression over rs56372821 genotypes (Hom Ref = GG; He = AG; Homo Alt = AA), for individuals in the GTEx database (The GTEx Consortium. Science, 2015, 348, 648–660). The major allele (G) is the risk allele for CUD. (picture downloaded from:

Supplementary Fig. 3 Quintile plots of Odds Ratio for CUD by PRS for cognitive performance/educational attainment.

Odds ratio (OR) for CUD by PRS within each quintile. The plots represent the three phenotypes related to cognitive/educational performance demonstrating significant association of PRS with CUD after correcting for multiple testing. Error bars indicate 95% confidence limits. A. OR for CUD by PRS for educational years (SSGAC) B. OR for CUD by PRS for college completion (SSGAC) C. OR for CUD by PRS for human intelligence

Supplementary Fig. 4 Gene expression of CHRNA2 and CNR1 in Allan Brain Atlas.

Gene expression of CHRNA2 and CNR1 in Allan Brain Atlas ( in 26 brain regions from 6 donors. Donors are marked in six different colors in the first row, and the 26 different regions are marked by different colors in the second row. Cerebellar cortex and cerebellar nuclei are marked with arrows. The results are shown in ‘Coarse’ mode, where the brain is divided into large neuroanatomical divisions or regions and the samples within each of the regions are averaged together to provide a summary value for the partition. The colors of the heat map are normalized expression values. The color green should be interpreted as relatively low expression and red as relatively high expression within the scope of each probe. There are two probes tagging CHRNA2 expression (both shown) and 89 probes tagging CNR1. The six probes tagging CNR1 expression demonstrating strongest negative correlation with CHRNA2 expression is shown (Pearson’s correlation coefficient, rmax = −0.498). 67% of the probes tagging CNR1 correlated with CHRNA2 expression with r > −0.4. (Picture downloaded from:,10021,12876,14380,15496,15697&search_type=correlation&search_term=&seed=1058207)

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Demontis, D., Rajagopal, V.M., Thorgeirsson, T.E. et al. Genome-wide association study implicates CHRNA2 in cannabis use disorder. Nat Neurosci 22, 1066–1074 (2019).

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