Table 1.
Summary of cis-eQTL and cis-meQTL signals identified in genome-wide analyses
| Cis-eQTL analysis (n = 992) | Cis-meQTL analysis (n = 337) | |
|---|---|---|
| Genome-wide SNPs (n = 8 639 940) | ||
| Tests conducted | 52 278 603 | 994 862 964 |
| Significant SNP-probe pairsa | 6788 | 77 664 |
| Unique lead SNPsb | 6526 | 64 483 |
| Significant eQTL/meQTL genes | 5632 | 13 325c |
Analyses were conducted using 22 793 expression probes, 423 604 methylation probes, and 8 639 940 genotyped and imputed SNPs. SNP and probes separated by <500 kb were tested for association
Beta distribution-adjusted empirical P-values from FastQTL were used to calculate q-values and a false-discovery rate (FDR) threshold of 0.01 was applied to identify eProbes/meCpGs with a significant eQTL/meQTL
a Counts include SNPs in high LD
b For the 6526 unique lead eSNPs, after pruning out one SNP of each SNP pair with linkage equilibrium r2 > 0.3, 5022 independent SNPs remain. For the unique lead 64 483 meSNPs, 29 472 independent SNPs remain by using the same pruning method
c n = 55 526 CpGs were assigned to a gene in Illumina annotation file