Table 2.

eQTL Effect of the Lead SNPs in Brain and Whole-Blood Tissues

Lead SNP Gene	Lead SNP	eQTL SNP	eQTL SNP Gene	r2	Tissue	Ref	Alt	Ensebl Gene ID	Minor Allele Samples	Minor Allele Count	MAF	p Value	Slope	Slope SE
ATXN3	rs10143310	rs2896190	TRIP11	1.00	brain cerebellar hemisphere	A	G	ENSG00000100815.12	78	90	0.26	6.8 × 10−7	0.24	0.05
ATXN3	rs10143310	rs2896190	TRIP11	1.00	brain cerebellum	A	G	ENSG00000100815.12	89	104	0.25	2.5 × 10−8	0.29	0.05
ATXN3	rs10143310	rs7142326	ATNX3	0.56	whole blood	T	C	ENSG00000066427.21	433	557	0.42	3.2 × 10−7	0.13	0.02
ATXN3	rs10143310	rs76497846	TRIP11	0.62	whole blood	G	A	ENSG00000100815.12	407	516	0.39	3.0 × 10−5	0.09	0.02
ATXN3	rs10143310	rs12587248	NDUFB1	0.62	whole blood	T	C	ENSG00000183648.9	356	423	0.32	2.5 × 10−8	0.10	0.02
B4GALNT1	rs12320537	rs2258877	B4GALNT1	0.88	brain cerebellar hemisphere	A	G	ENSG00000135454.13	79	92	0.26	1.7 × 10−7	0.24	0.04
B4GALNT1	rs12320537	rs2258877	B4GALNT1	0.88	brain cerebellum	A	G	ENSG00000135454.13	95	106	0.25	1.8 × 10−5	0.18	0.04
B4GALNT1	rs12320537	rs12322482	ATP23	0.99	whole blood	G	A	ENSG00000166896.7	245	272	0.20	1.4 × 10−10	−0.29	0.04
SCFD1	rs229247	rs7154847	SCFD1	0.89	Brain anterior cingulate cortex BA24	G	A	ENSG00000092108.20	82	101	0.34	3.3 × 10−7	0.33	0.06
SCFD1	rs229247	rs229231	SCFD1	0.99	brain cerebellar hemisphere	G	A	ENSG00000092108.20	107	143	0.41	3.1 × 10−16	0.33	0.03
SCFD1	rs229247	rs229152	SCFD1	0.94	brain cerebellum	T	C	ENSG00000092108.20	126	164	0.39	2.2 × 10−24	0.37	0.03
SCFD1	rs229247	rs229173	SCFD1	0.95	brain cortex	T	C	ENSG00000092108.20	123	159	0.39	2.1 × 10−7	0.23	0.04
SCFD1	rs229247	rs10130830	SCFD1	0.91	brain frontal cortex BA9	A	G	ENSG00000092108.20	113	146	0.42	1.4 × 10−8	0.27	0.05
SCFD1	rs229247	rs448175	SCFD1	1.00	whole blood	G	T	ENSG00000092108.20	415	536	0.40	1.9 × 10−56	−0.28	0.02
ACSL5	rs58854276	rs2419629	ZDHHC6	0.90	brain cerebellum	A	G	ENSG00000023041.11	113	144	0.34	2.1 × 10−7	0.28	0.05
ACSL5	rs58854276	rs72821869	ZDHHC6	0.84	brain cortex	C	T	ENSG00000023041.11	121	152	0.37	7.6 × 10−6	0.29	0.06
ACSL5	rs58854276	rs12414780	ZDHHC6	0.83	brain frontal cortex BA9	C	G	ENSG00000023041.11	100	123	0.36	3.2 × 10−7	0.41	0.08
ACSL5	rs58854276	rs2419629	ZDHHC6	0.90	brain nucleus accumbens basal ganglia	A	G	ENSG00000023041.11	120	151	0.37	1.9 × 10−8	0.40	0.07
ACSL5	rs58854276	rs12414780	ZDHHC6	0.83	brain putamen basal ganglia	C	G	ENSG00000023041.11	101	129	0.38	1.3 × 10−5	0.34	0.08
ACSL5	rs58854276	rs72821869	ACSL5	0.84	whole blood	C	T	ENSG00000197142.10	356	446	0.33	3.2 × 10−48	−0.38	0.02

For each lead SNP, we reported the most significant eQTLs from GTEx in LD (r² > 0.5) with the lead SNP. For each eQTL, we reported the the r² with the corresponding lead SNP, the tissue in which the effect was observed, the corresponding regulated gene, the number of samples carrying the minor allele, the total number of minor alleles, the minor allele frequency, the p value, and regression slope and its standard error. The data are from GTEx version 8.