Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies

Table 2 Number of independent, significant eQTL-gene pairs with number of unique eQTLs or unique genes with P value corresponding to indicated FDR cutoff

Pair type	eQTL-TranscriptCluster pairs	Unique eQTLs	Independent pairs	Independent unique lead eQTLs	Unique genes^a(% available)	P value cutoff
Nominal FDR < 0.05
Cis	4,285,456	2,221,013	19,613	19,239	10,327 (58%)	1.00 E-4*
Trans	216,169	91,559	6741	5749	4958 (28%)	1.41 E-7
Nominal FDR < 0.0005
Cis	3,698,429	2,008,734	17,452	17,119	9232 (52%)	1.78E-5
Trans	116,960	52,426	1464	888	1025 (6%)	8.82E-10
Available	1.521 E11	8,510,936	1.521 E11	8,510,936	17,873 (100%)

*P value cutoff corresponding to FDR. Upper bound P value for pairs retained in computation was 1E-4, therefore highest attained FDR for cis-eQTLs was 0.0024
^aTranscript cluster ID is used as a proxy for genes. Only 244 genes were represented by more than one Transcript cluster IDs. Approximately 270 Transcript cluster IDs could not be assigned to an Entrez Gene entry

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