. 2017 Aug 1;7(8):e1188. doi: 10.1038/tp.2017.159

Table 1. LD-independent SNPs with P-values smaller than 1.25 × 10⁻⁶.

Tissue volume	Chr	Best SNP	A1	A2	MAF	Effect size	Likelihood ratio	P-value	Variance explained	Diff./allele	Closest protein coding gene (±500 kb)
ICV	15	rs8030297	T	G	0.07	−32 231	28.46	9.56E−08	2.47	−6.73	KLF13
	20	rs4809613	A	G	0.17	−19 053	24.38	7.91E−07	0.36	−3.98	EYA2
	3	rs9831671	T	G	0.27	20 450	24.03	9.49E−07	0.43	4.27	LMCD1
WM	16	rs10514437	G	A	0.03	−6617	31.97	1.56E−08	4.14	−3.76	WWOX
	20	rs117068934	G	A	0.03	−5988	26.34	2.86E−07	1.01	−3.41	SLC13A3
	6	rs9361254	G	T	0.13	−3106	24.10	9.16E−07	0.31	−1.77	MEI4a, HTR1B
	18	rs138549714	G	GT	0.07	−3608	23.96	9.85E−07	0.29	−2.05	MYOM1
	12	rs11834561	G	A	0.38	2071	23.92	1.00E−06	0.29	1.18	USP44
	21	rs200193477	A	AT	0.26	3577	23.66	1.15E−06	0.27	2.03	—
GM	4	rs114518130b	G	A	0.01	14 973	39.04	4.15E−10	6.52	6.13	IGFBP7
	7	rs7786147	C	T	0.11	−4135	28.10	1.15E−07	2.27	−1.69	MPLKIPc
	3	rs200355458	C	CG	0.09	4657	27.74	1.39E−07	1.86	1.91	OPA1
	8	rs2565117	C	A	0.01	−10 939	26.33	2.88E−07	1.12	−4.48	ZMAT4
	18	rs138087875	A	AC	0.06	4789	25.78	3.83E−07	0.60	1.96	CNDP1
	16	rs12919005	C	G	0.03	6973	25.55	4.31E−07	0.51	2.85	TOX3
	9	rs77196186	C	T	0.05	−4970	24.77	6.45E−07	0.40	−2.03	CAAP1
	16	rs9889138	G	A	0.07	4482	24.39	7.86E−07	0.34	1.83	C16orf62
	14	rs1092055	T	C	0.45	2142	24.28	8.32E−07	0.34	0.88	SLC35F4
	10	rs11012877	G	A	0.11	3683	24.23	8.54E−07	0.33	1.51	CACNB2
	1	rs2992041	C	T	0.43	2516	24.05	9.37E−07	0.32	1.03	CTH
	16	rs7206373	G	C	0.46	2084	23.77	1.09E−06	0.29	0.85	SEC14L5
CSF	16	rs7195044	C	G	0.09	5619	26.55	2.56E−07	1.33	9.54	RBFOX1
	17	rs11867179	C	G	0.24	3042	25.43	4.6E−07	0.53	5.17	TBX4
	4	rs113668862	C	T	0.08	−4951	24.95	5.9E−07	0.43	−8.41	FRG1
	18	rs11875537	T	G	0.44	2559	24.35	8.05E−07	0.37	4.35	METTL4

Abbreviations: CSF, cerebrospinal fluid; GM, gray matter; ICV, intracranial volume; LD, linkage disequalibrium; MAF, minor allele frequency; SNP, single-nucleotide polymorphism; WM, white matter.

Provisional or inferred status in RefSeq (next closest protein coding gene within 500 kb is also listed).

Genome-wide significant (P<1.25 × 10⁻⁸), Bonferroni correction of 5 × 10⁻⁸ for four phenotypes.

Also known as c7orf11.

Note that all SNPs are imputed with the exception of rs10514437; see Supplementary Figure 2 for a genotyping cluster plot of rs10514437. A1 is the effective allele and A2 is the reference allele. Diff./allele is the ratio of effect size over mean brain volume.

We define LD-independent SNPs as those with low LD (r²<0.1) to a more significantly associated SNP within a 500 kb window.

Table 1. LD-independent SNPs with P-values smaller than 1.25 × 10−6.

Table 1. LD-independent SNPs with P-values smaller than 1.25 × 10⁻⁶.