Table 1 Descriptive characteristics, meQTL query parameters, and meQTL summary results for four tissues examined

	Sample size	Meth SD cutoff^a	SNP MAF threshold^b	Max SNP to CpG distance^c	meQTL P value thresholds^d	# of meQTLs identified	# of meQTL targets identified
Fetal brain^e	166	NA	5%	1 Mb	1.0e–08^f	299,992^f	7863^f
Peripheral blood	339	0.15	2.75%	1 Mb	3.1e–05^g	2,003,443^g	95,195^g
					1.0e–05^h	1,878,577^h	85,250^h
					3.0e–07ⁱ	1,598,033ⁱ	68,860ⁱ
Cord blood	121	0.15	7%	500 Kb	8.5e–06^g	1,374,554^g	41,681^g
					2.7e–06^h	1,252,498^h	35,905^h
					2.0e–07ⁱ	1,032,370ⁱ	28,423ⁱ
Lung^e	210	NA	3%	500 Kb	4.0e–05^h	22,866^h	34,304^h

^aThe probe standard deviation across samples that was used as an inclusion criterion for CpG sites in the meQTL query (blood data sets only)
^bThe MAF cutoff used as an inclusion criterion for SNPs in the meQTL query
^cThe maximum distance between the SNP and CpG site used in the meQTL query for the peripheral blood, cord blood, and lung data sets, and the value at which results for filtered in the fetal brain results
^dSNP-to-CpG association P values considered in subsequent analyses
^ePublicly available data
^fFDR not specified
^gFDR = 10%
^hFDR = 5%
ⁱFDR = 1%

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