Skip to main content

Table 2 Traits and diseases from the NHGRI GWAS catalog with associated loci enriched for local meQTLs

From: High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction

Phenotype N annot Overlap Fisher PV OR Perm Z Perm PV Perm QV
Bone mineral density 25 15 1.58E-07 9.03 6.530 4.40E-10 1.07E-07
Breast cancer 34 17 8.28E-07 6.02 5.878 2.51E-08 3.05E-06
Blood pressure 9 7 3.28E-05 21.06 5.551 1.63E-07 1.31E-05
Height 90 31 1.25E-06 3.16 5.499 2.16E-07 1.31E-05
Major depressive disorder 14 9 2.44E-05 10.84 5.452 2.80E-07 1.36E-05
Non-alcoholic fatty liver disease 7 6 5.13E-05 36.10 5.413 3.47E-07 1.41E-05
Alzheimer’s disease 17 10 2.54E-05 8.60 5.203 1.06E-06 3.67E-05
Rheumatoid arthritis 37 16 1.84E-05 4.59 5.167 1.27E-06 3.86E-05
Hypertension 10 7 9.59E-05 14.05 5.010 2.82E-06 7.62E-05
QRS duration 8 6 1.80E-04 18.06 4.911 4.62E-06 1.08E-04
Crohn’s disease 42 17 2.89E-05 4.09 4.900 4.89E-06 1.08E-04
Pulmonary function decline 6 5 3.10E-04 30.10 4.803 7.79E-06 1.58E-04
IgG glycosylation 70 23 8.67E-05 2.95 4.409 4.80E-05 8.98E-04
Systemic lupus erythematosus 15 8 4.25E-04 6.88 4.199 1.18E-04 1.93E-03
Bone mineral density — spine 5 4 1.82E-03 24.08 4.198 1.19E-04 1.93E-03
Hip geometry 5 4 1.82E-03 24.08 4.173 1.32E-04 2.01E-03
Autism spectrum, attention deficit-hyperactivity, bipolar and major depressive disorders and schizophrenia combined 19 9 5.72E-04 5.42 4.103 1.77E-04 2.52E-03
Mean corpuscular hemoglobin 5 4 1.82E-03 24.08 4.084 1.90E-04 2.57E-03
Tuberculosis 8 5 2.25E-03 10.03 4.031 2.36E-04 3.02E-03
Bipolar disorder and schizophrenia 24 10 9.86E-04 4.30 3.799 5.85E-04 7.11E-03
Obesity-related traits 165 40 7.21E-04 1.93 3.709 8.22E-04 9.52E-03
  1. We examined 494,420 meQTLs out of 3,470,923 methylation sites, after removal of sites in regions flagged as copy number variants, genomic duplications or pseudogenes. We consider local meQTLs and do not stratify by presence or absence of CpG-SNPs at the meQTL site. “N annot” is the number of loci in the NHGRI GWAS catalog for that trait or disease, “Overlap” is the number of GWAS loci that overlap with a local meQTL, “Fisher PV” is the p value from the Fisher exact test of enrichment, “OR” is the odds ratio, “Perm Z” is the Z-statistic of the permutation test, “Perm PV” is the p value from >300,000 permutations, “Perm QV” is the q value of the permutation test. Only findings passing FDR control with q value < 0.01 are shown