Table 1 Functional annotation of genetic findings provides insight into the molecular mechanisms underlying statistical associations.

From: The genetic aetiology of cannabis use: from twin models to genome-wide association studies and beyond

Phenotype	Study	Lead SNP	Chr	Position (base pair)	A1	A2	Freq A1	Effect size^a	SE	p-value	N	Nearby genes/transcripts	Functional annotation
Phenotype	Study	Lead SNP	Chr	Position (base pair)	A1	A2	Freq A1	Effect size^a	SE	p-value	N	Nearby genes/transcripts	Method	Annotated gene(s)
Cannabis initiation	Pasman et al. [75]	rs2875907	3	85518580	A	G	0.352	0.070	0.009	9.38e−17	181,675	CADM2	MAGMA	35 genes (NCAM1 and CADM2 among top findings)
		rs1448602	3	85780454	A	G	0.756	−0.062	0.010	6.55e−11	184,765	CADM2	TWAS (PrediXcan)	21 genes (CADM2 among top findings)
		rs7651996	3	85057349	T	G	0.477	0.049	0.008	2.37e−09	184,765	CADM2
		rs10085617	7	3634711	A	T	0.416	0.046	0.008	2.93e−08	184,765	SDK1
		rs9773390	8	81565692	T	C	0.933	−0.171	0.029	5.66e−09	44,595	ZNF704
		rs9919557	11	112877408	T	C	0.614	−0.055	0.009	9.94e−11	180,428	NCAM1
		rs10499	16	28915527	A	G	0.651	0.053	0.009	1.13e−09	179,767	RABEP2; ATP2A1
		rs17761723	17	2107090	T	C	0.346	0.047	0.009	3.24e−08	184,765	SMG6
Age at first cannabis use	Minică et al. [29]	rs1574587	16	84453056	T	C	0.142	0.090	0.016	4.0e−09	24,953	ATP2C2	GATES gene-based analysis	ATP2C2
Cannabis dependence^a	Agrawal et al. [96]	rs77300175	10	120633376	T	C	0.050^b	0.530	0.09	1.3e−08	2080 cases 6435 controls	12 genes within regulatory domain	Genomic and epigenomic annotation of rs1409568	Located within active enhancer; enrichment of H3K27ac marks; predicted to bear active enhancer marks in brain-derived tissues; changes of CpG methylation of TIAL1; Association with hippocampal volume in college students
Cannabis Dependence (criterion count)	Sherva et al. [76]	rs143244591	3	149013935	G	A	0.96	0.54	NA	4.32 × 10⁻¹⁰	6000 African American and 8754 European American participants	RP11-206M11.7	NA	NA
		rs146091982	10	95659958	A	G	0.95	0.54	NA	1.33 × 10⁻⁹		SLC35G1
		rs77378271	8	3073489	A	G	0.95	0.29	NA	2.13 × 10⁻⁸		CSMD1
Cannabis use disorder	Johnson et al. [78]	rs7783012	7	114116881	A	G	0.569^b	0.104	0.02	1·84 × 10⁻⁹	17,068 cases, 357,219 controls	FOXP2	eQTL analysis	FOXP2
		rs4732724	8	27432062	C	G	0.214^b	−0.117	0.02	6·46 × 10⁻⁹	Half of the sample	CHRNA2; EPHX2	eQTL analysis	CHRNA2; EPHX2; CCDC25; CLU; STMN4
													MAGMA^c	FOXP2; PDE4B; ENO4
													TWAS (PrediXcan)	NAT6; HYAL3; IFRD2

SNP single nucleotide polymorphism, Chr chromosome.
^cJohnson et al. also report H-MAGMA results [146], but have been excluded here as these results may include an excessive number of false positive findings due to incorrect specification of the null distribution in MAGMA; a problem that has been resolved in the latest MAGMA version.
^aFor this GWAS, the control sample was selected to have used cannabis during their life (i.e. those who had never used cannabis were excluded from analyses).
^bNote that these A1 allele frequencies were obtained from https://www.ncbi.nlm.nih.gov/snp/ (European estimates), whereas for the other SNPs the A1 allele frequencies were reported in the original GWASs, as obtained from the included samples.

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Table 1 Functional annotation of genetic findings provides insight into the molecular mechanisms underlying statistical associations.

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