Table 2 Methods and conclusions from studies of cis-acting mQTLs

Cerebellum (153)

Illumina 27 K Methyl; Affy 5.0 SNP chips; validation by Pyroseq; eQTLs:Affy HGU95Av2

mQTLs detected at ~8% of the CpGs; mQTL CpGs enriched in CGIs and within 150 kb of the index SNP; 13% of mQTL index SNPs associated with eQTLs

[62]

Brains (150 individuals; 4 brain regions)

Illumina 27 K Methyl; Illumina 550 K SNP chips; eQTLs: Illumina HumanRef-8

mQTLs detected at ~5% of CpGs. mQTL CpGs were depleted in CGIs. ~50% of the mQTLs were detected only in one brain region. ~5% of the index SNPs were both mQTLs and eQTLs

[108]

Adipose tissue (648), replication set PBL (200)

Illumina 450 K Methyl; multiple genotyping arrays, eQTLs: HT-12 V3 BeadChips; validations by WGBS

mQTLs detected at ~28% the CpGs, with tissue-specificity; 22% of eQTLs were in LD with at least one mQTL; ~4% were in LD with a GWAS SNP; mQTLs associated with eQTLs and GWAS SNPs were enriched in enhancers

[110]

Cord blood (174), PBL (90), TC (125), FC (111), pons (106), cerebellum (105)

Illumina: 27 K Methyl BeadChips; multiple Illumina and Affy genotyping arrays

mQTLs detected at ~5% of the CpGs; overlap observed between ancestral groups, developmental stages, and tissue types; brain mQTL SNPs enriched in bipolar disorder GWAS peaks and miRNA-binding sites

[155]

TC (44), neurons (18), glia (22), T-cells (54), placenta (37)

Illumina 450 K Methyl and 2.5 M SNP chips; validation by bis-seq and ox-bis-seq

~3000 strong mQTLs identified; more than half tissue-restricted and ~900 located near GWAS signals; mQTLs enriched in polymorphic CTCF-binding sites and TFBS, and enriched in eQTLs located within 20 kb

[49]

Fetal brain (166), matched adult PFC, striatum and cerebellum (83)

Illumina 450 K Methyl; 2.5 M SNP chips

Most fetal mQTLs also present in adult brain, but ~1/3 showed differential effects; mQTLs enriched in repressive and poised histone marks; mQTLs enriched in CTCF motifs, eQTLs, and schizophrenia-associated GWAS peaks

[112]

PBL (85)

Illumina 27 K Methyl; OmniExpress SNP chips

1287 smoking associated DM CpGs and 770 mQTLs identified. Among these, 43 CpGs were both smoking DM and mQTL

[150]

Adipose tissue (119)

Illumina 450 K Methyl; Omni SNP chips; eQTL:Affymetrix Human Gene 1.0 ST array

mQTLs detected in ~3% of the CpGs; enriched in CGI shelves and shores and depleted in promoter regions and CGI; ~1% of mQTL SNPs (or proxy) were obesity-associated GWAS SNPs; 2% of the SNPs showed both mQTL and eQTL

[113]

CD4+ T cells (717)

Illumina 450 K Methyl; Affy 6.0 SNP chips

Of ~20,000 heritable CpGs identified by modeling family structure, 15,133 were cis-mQTLs; 1329 trans-mQTLs and 4113 CpGs showing no evidence of cis or trans mQTL

[54]

Monocytes (197), neutrophils (197), and CD4+ T cells (132)

Illumina 450 K Methyl; WGS; RNA-seq for ASE and ChIP-seq for hQTLs

mQTLs affect 10% of CpGs, hQTLs found in 28 and 12% of H3K4me1 and H3K27ac peaks; 345 GWAS index SNPs (or SNPs in high LD with a GWAS index SNPs) colocalized with mQTLs and/or hQTLs

[37]