Table 2.

Replication rates between GTEx and publicly available eQTL from these analyses.

GTEx Brain Region	# eQTL	Replication (π1) of GTEx eQTL				Replication (π1) of AMP-AD eQTL in GTEx
		Meta-Analysis	ROSMAP	Mayo TCX	Mayo CER	Meta-Analysis	ROSMAP	Mayo TCX	Mayo CER
Amygdala	158,270	0.974	0.987	0.986	0.916	0.356	0.421	0.701	0.555
Anterior Cingulate Cortex (BA24)	291,898	0.976	0.971	0.962	0.903	0.445	0.516	0.772	0.592
Caudate Basal Ganglia	435,939	0.966	0.961	0.935	0.881	0.488	0.544	0.781	0.636
Cerebellar Hemisphere	575,583	0.896	0.897	0.781	0.962	0.458	0.509	0.719	0.831
Cerebellum	819,435	0.893	0.890	0.711	0.936	0.526	0.577	0.761	0.863
Cortex	478,903	0.980	0.973	0.941	0.892	0.547	0.604	0.834	0.659
Frontal Cortex (BA9)	342,988	0.974	0.967	0.963	0.897	0.489	0.547	0.792	0.632
Hippocampus	221,876	0.967	0.970	0.937	0.905	0.404	0.462	0.710	0.570
Hypothalamus	227,808	0.974	0.966	0.960	0.913	0.392	0.436	0.719	0.580
Nucleus Accumbens Basal Ganglia	376,390	0.958	0.952	0.781	0.894	0.453	0.514	0.761	0.622
Putamen Basal Ganglia	293,880	0.966	0.974	0.930	0.890	0.433	0.493	0.764	0.591
Spinal Cord Cervical (c-1)	175,702	0.940	0.952	0.918	0.862	0.330	0.394	0.640	0.514
Substantia Nigra	120,582	0.964	0.951	0.960	0.928	0.297	0.372	0.635	0.479