Table 1 ∣.

Genome-wide association results for subcortical brain volumes in Europeans from the CHARGE and ENIGMA consortia and UK Biobank

SNP	Chromosome	Position	Function	A1/A2	A1 frequency	Weight (SNP n)	Z score	P valuea	Directionb	I2c
Nucleus accumbens (n = 32,562)
rs9818981d	3	190,602,087	Intergenic	A/G	0.09	32,282	−6.23	4.70 × 10−10	−−−	63.2
rs13107325	4	103,188,709	Missense	T/C	0.06	32,283	6.15	7.74 × 10−10	+++	76.2
rs11747514d	5	65,839,259	Intronic	T/G	0.22	32,562	−5.99	2.11 × 10−9	−−−	0
rs868202d	14	56,195,762	Intergenic	T/C	0.56	32,562	5.90	3.55 × 10−9	+++	0
Amygdala (n = 34,431)
rs11111293d	12	102,921,296	Intergenic	T/C	0.78	34,313	6.25	4.16 × 10−10	+++	0
Brainstem (n = 28,809)
rs11111090	12	102,326,461	Intergenic	A/C	0.52	28,809	10.79	3.70 × 10−27	+++	0
rs10217651d	9	118,923,652	Intronic	A/G	0.39	28,809	9.78	1.40 × 10−22	+++	0
rs869640d	5	65,015,128	Intronic	A/C	0.72	28,809	−8.40	4.36 × 10−17	−−−	9.5
rs9398173d	6	109,000,316	Intronic	T/C	0.33	28,809	−7.95	1.80 × 10−15	−−−	19.0
rs10792032d	11	68,984,602	Intergenic	A/G	0.49	28,648	7.75	9.08 × 10−15	+++	39.4
rs4396983d	4	15,132,604	Intergenic	A/G	0.44	28,809	−7.02	2.27 × 10−12	−−−	73.6
rs9322194d	6	149,920,249	Intronic	T/C	0.34	28,156	6.91	4.94 × 10−12	+++	0
rs7972561d	12	107,139,983	Intronic	A/T	0.33	28,809	6.90	5.05 × 10−12	+++	0
rs2206656d	20	49,130,119	Intronic	C/G	0.61	28,809	6.83	8.26 × 10−12	+++	0
rs12479469d	20	61,145,196	Intergenic	A/G	0.33	25,822	−6.80	1.08 × 10−11	−−−	65.6
rs4784256d	16	52,814,559	Intergenic	A/G	0.40	28,809	6.76	1.41 × 10−11	+++	0
rs555925d	3	193,544,359	intergenic	T/G	0.41	27,934	6.37	1.88 × 10−10	+++	62.9
rs12313279d	12	102,846,504	Intronic	A/G	0.29	28,809	6.21	5.39 × 10−10	+++	24.9
rs9505301d	6	7,887,131	Intronic	A/G	0.89	28,691	−6.05	1.41 × 10−9	−−−	43.2
rs11684404d	2	88,924,622	Intronic	T/C	0.66	28,809	−5.95	2.73 × 10−9	−−−	0
rs112178027d	17	27,564,013	Intergenic	T/C	0.17	28,809	−5.90	3.67 × 10−9	−−−	0
Caudate nucleus (n = 37,741)
rs3133370	11	92,026,446	Intergenic	T/C	0.67	37,741	7.52	5.59 × 10−14	+++	44.9
rs6060983d	20	30,420,924	Intronic	T/C	0.70	37,741	7.04	1.95 × 10−12	+++	0
rs7040561d	9	128,528,978	Intronic	A/T	0.85	34,049	−6.26	3.84 × 10−10	−−−	0
rs2817145d	1	3,133,422	Intronic	A/T	0.19	35,598	6.20	5.71 × 10−10	+++	65.3
rs148470213d	14	56,193,700	Intergenic	T/C	0.54	29,429	6.18	6.48 × 10−10	++?	0
rs1987471d	16	28,825,866	Intergenic	T/G	0.63	37,741	5.87	4.40 × 10−9	+++	0
rs12445022d	16	87,575,332	Intergenic	A/G	0.33	37,741	5.87	4.45 × 10−9	+++	0
rs55989340d	14	100,635,222	Intergenic	A/G	0.74	37,741	−5.86	4.62 × 10−9	−−−	52.0
rs4888010d	16	73,895,046	Intergenic	A/G	0.47	37,741	5.86	4.67 × 10−9	+++	74.9
rs35305377d	7	99,938,955	Intronic	A/G	0.55	33,429	−5.84	5.36 × 10−9	−−−	47.8
Globus pallidus (n = 34,413)
rs2923447	8	42,439,848	Intergenic	T/G	0.59	34,413	8.11	4.88 × 10−16	+++	34.0
rs10129414d	14	56,193,272	Intergenic	A/G	0.44	34,413	−7.53	5.11 × 10−14	−−−	0
rs196807d	8	24,682,649	Intergenic	A/G	0.18	34,295	6.44	1.17 × 10−10	+++	21.1
rs10439607d	20	30,258,541	Intronic	A/G	0.30	34,413	−6.28	3.35 × 10−10	−−−	0
rs4952211d	2	32,611,512	Intronic	T/C	0.43	34,252	−5.86	4.72 × 10−9	−−−	61.9
rs12567402d	1	21,870,213	Intronic	T/C	0.33	34,214	5.81	6.17 × 10−9	+++	0
Putamen (n = 37,571)
rs945270	14	56,200,473	Intergenic	C/G	0.58	37,571	15.03	5.02 × 10−51	+++	57.3
rs62098013	18	50,863,861	Intronic	A/G	0.38	37,571	8.92	4.59 × 10−19	+++	33.9
rs6087771	20	30,306,724	Intronic	T/C	0.71	36,291	8.69	3.75 × 10−18	+++	7.5
rs35200015d	11	117,383,215	Intronic	A/G	0.19	37,571	−8.19	2.51 × 10−16	−−−	0
rs1432054	11	83,260,225	Intronic	A/G	0.64	37,571	−7.94	2.10 × 10−15	−−−	0
rs7902527d	10	118,715,399	Intronic	A/G	0.24	37,108	6.29	3.13 × 10−10	+++	0
rs2244479d	7	50,738,987	Intronic	T/C	0.65	36,291	−5.92	3.17 × 10−9	−−−	32.1
rs2410767d	5	87,705,268	Intronic	C/G	0.78	37,571	5.88	3.99 × 10−9	+++	0
rs1187162d	11	92,011,126	Intergenic	T/C	0.42	37,571	5.84	5.14 × 10−9	+++	0
Thalamus (n = 34,464)
rs12600720d	17	78,448,640	Intronic	C/G	0.69	33,023	6.25	4.06 × 10−10	+++	0
rs142461330d	7	55,012,097	Intergenic	T/C	0.92	34,185	−5.90	3.69 × 10−9	−−−	0

Linear regression models are adjusted for sex, age, age², total intracranial volume (CHARGE and ENIGMA) or total brain volume (UK Biobank), and population stratification.

^aP values are two tailed. Significance was set at P < 8.3 × 10⁻⁹ after additional Bonferroni correction for six independent traits (5 × 10⁻⁸/6).

^bDirection of association, ordered as CHARGE, ENIGMA, and UK Biobank.

^cHeterogeneity as estimated proportion of total variance.

^dNovel SNPs. A1, coded allele; A2, non-coded allele.