Here are listed in tables the GENCORD2 discovered eQTLs, mQTLs and eQTMs at 10% FDR for each cell-type (fibroblasts, F; lymphoblastoid, L; T-cells, T).
Note that for eQTMs, although in the table of the article the number of discovered genes with these associations at 10%FDR is reported, we are providing a list of all the
methylation sites associated to each gene given that their correlation structure is not as strong as that for genetic variants and may be useful to have this information.
Please see the Materials and Methods section for details.
All coordinates based on hg19.
Gene annotation: Gencode V10 (exon coordinates correspond to merged exons from the annotated transcripts of a gene)

Columns:

EQTL files:

SNP_label = SNP ID
GENE_ID = Ensembl Gene ID and exon start and end coordinates
SNP_chromosome = SNP chromosome
GENE_chromosome = gene chromosome
SNP_location = SNP position
GENE_location = transcription start site of gene
Distance = distance from SNP to transcription start site
rvalue = Spearman correlation coefficient
pvalue = P-value
-log10(pvalue) = -log10(P-value)

MQTL files:

SNP_label = SNP ID
METHYL_ID = methylation site probe ID
SNP_chromosome = SNP chromosome
METHYL_chromosome = methylation site chromosome
SNP_location = SNP position
METHYL_location = methylation site position
Distance = distance from SNP to methylation site
rvalue = Spearman correlation coefficient
pvalue = P-value
-log10(pvalue) = -log10(P-value)

EQTM files:

METHYL_label = methylation site probe ID
GENE_ID = Ensembl Gene ID and exon start and end coordinates
METHYL_chromosome = methylation site chromosome
GENE_chromosome = gene chromosome
METHYL_location = methylation site position
GENE_location = transcription start site of gene
Distance = distance from methylation site to transcription start site
rvalue = Spearman correlation coefficient
pvalue = P-value
-log10(pvalue) = -log10(P-value)
