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Table 1 Summary of eQTL mapping results. FDR is estimated using Benjamini–Hochberg procedure

From: A pipeline for RNA-seq based eQTL analysis with automated quality control procedures

Summary Threshods ROSMAP Mayo MSBB CommonMind
Effective sample size NA 334 103 65 200
Gene count NA 26,663 27,101 29,736 21,511
Variant count NA 6,736,714 6,932,711 6,937,313 6,703,202
Top PC count NA 3 3 3 3
Cis-eQTL associations \(P<1\) 124,877,625 131,696,349 143,560,218 103,667,853
Trans-eQTL associations \(P<10^{-4}\) 18,617,087 19,594,408 21,324,856 14,353,808
Cis-eQTL associations \(FDR<0.05\) 3,132,119 516,977 124,675 404,182
Cis-eQTL count \(FDR<0.05\) 1,515,726 326,652 78,690 306,100
Cis-gene count \(FDR<0.05\) 21,173 7999 3373 6021
Trans-eQTL associations \(FDR<0.05\) 163,821 23,200 13,000 9151
Trans-eQTL count \(FDR<0.05\) 78,894 13,607 6454 8914
Trans-gene count \(FDR<0.05\) 3079 745 394 203