Table 3:

Top variants in each region that met genome-wide significance.

Phenotype	CHR	BP	variant	Gene	Minor Allele	Major Allele	AA MAF	EA MAF	EA P value	COGA AA+EA P value	Yale- Penn-AA P value	SAGE- AA P value	SAGE EA P value	OZALC EA P value	Meta P value	Direction
DSM -IV AD	1	174,637,937	rs61826952	RABGAP1L	G	A	0.10	0.07	7.73E-06	8.42E-11	0.01	0.13	0.46	0.24	1.66E-04	−−++−−
Time spent drinking	2	123,424,651	rs7597960	TSN,LINC01826	T	A	0.65	0.21	4.43E-06	1.22E-08	0.23	8.94E-03	0.83	0.33	8.86E-05	−−−+−+
DSM -IV AD	4	100,239,319	rs1229984	ADH1B	T	C	0.01	0.03	2.09E-07	1.72E-08	0.82	0.11	0.54	0.01	5.30E-09	−−+−−−
DSM -IV AD criterion count	4	100,239,319	rs1229984	ADH1B	T	C	0.01	0.03	4.16E-11	2.61E-13	0.86	0.01	0.10	0.06	4.09E-10	−−+−−−
Desire to cut drinking	4	100,239,319	rs1229984	ADH1B	T	C	0.01	0.03	1.21E-11	6.01E-14	0.82	0.03	4.89 E-03	5.52E-03	9.79E-18	−−+−−−
Tolerance	4	100,239,319	rs1229984	ADH1B	T	C	0.01	0.03	1.89E-07	8.06E-09	0.95	7.31E-03	0.32	0.14	1.20E-09	−−−−−−
Drinking more than intended	8	127,213,398	rs188227250	LINC00861, LOC101927657	A	G	0.02	0.03	6.72E-09	1.03E-06	-	-	0.91	1.96E-03	3.71E-09	+−+
Time spent drinking	15	36,344,539	rs1912461	MIR4510,C15orf41	C	T	0.02	0.01	1.77E-08	1.60E-05	-	-	0.18	0.12	2.31E-08	+++

Minor allele is defined as minor allele in EA samples. Directions of effect are in terms of minor alleles with + and – meaning increasing or decreasing the chance of having AD or DSM-IV AD criterion, or the number of DSM-IV AD criterion count. For significant findings in COGA AA+EA, the order of directions are: COGA AA, EA, Yale-Penn-AA, SAGE-AA, SAGE-EA, OZALC-EA; for significant findings in EA, the order of directions are: EA, SAGE-EA, OZALC-EA.