Published October 27, 2023 | Version v1
Dataset Open

AdipoExpress: Adipose eQTL meta-analysis summary statistics

Creators

  • 1. University of North Carolina at Chapel Hill
  • 2. ROR icon King's College London
  • 3. ROR icon University of Michigan–Ann Arbor

Description

Datasets linked to the publication titled: "Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits"

Summary statistics from the eQTL meta-analysis of five subcutaneous adipose tissue datasets (AdipoExpress). 

  1. Supplemental tables 3, 4, 10, and 11 with the list of eQTL signals (lead variants per gene per signal)
  2. Supplemental tables 20 and 25 with the list of GWAS-eQTL colocalized signals
  3. Full marginal eQTL summary statistics (marginal_byChr_*.tar.gz)
  4. All-but-one conditional eQTL summary statistics (AB1_byChr_*.tar.gz)

 

Supplemental tables 3, 4, 10, and 11 with the list of eQTL signals (lead variants per gene per signal)

Column label Column description
ENSG Ensembl ID for gene GENCODE v19
gene Gene symbol
studies Studies with gene expressed. 1=METSIM (N), 2=METSIM (S), 3=FUSION, 4=TwinsUK, 5=GTEx (1=FUSION, 2=GTEx sex-stratified)
signal Signal number for the row : the total number of signals for that gene
variant Chromosome_position_NonEffectAllele_EffectAllele
beta Variant to gene effect for the joint model with all signals
se Standard error
pval_joint p-value of the joint model with all the eQTL variants that pass the 1e-6 stepwise threshold (*Used in the manuscript)
pval_signal p-value calculated with ACAT to correct for the number of variants per gene and is based on all the variants in a signal
pval_marginal p-value from the single-variant (marginal) meta-analysis
pval_stepwise p-value for the lead variant, conditioned on the previously selected variants

 

Full marginal eQTL summary statistics (marginal_byChr_*.tar.gz)

Column label Column description
chr Chromosome
pos Position (hg19)
ref Reference allele (non-effect allele)
alt Alternative allele (effect allele)
SNP Chromosome_position_NonEffectAllele_EffectAllele
ENSG Ensembl ID for gene GENCODE v19
gene Gene symbol
studies Studies with gene expressed. 1=METSIM (N), 2=METSIM (S), 3=FUSION, 4=TwinsUK, 5=GTEx (1=FUSION, 2=GTEx sex-stratified)
beta Effect size of association between variant and gene
se Standard error
pval p-value of association between variant and gene
N  

 

All-but-one conditional eQTL summary statistics (AB1_byChr_*.tar.gz)

Column label Column description
gene Gene symbol
ENSG Ensembl ID for gene GENCODE v19
SNP Chromosome_position_NonEffectAllele_EffectAllele
ref Reference allele (non-effect allele)
alt Alternative allele (effect allele)
beta Effect size of association between variant and gene
se Standard error
pval p-value of association between variant and gene
lead_SNP Lead SNP for the signal
EAF Effect allele frequency
SNP_N SNP sample size
studies Studies with gene expressed. 1=METSIM (N), 2=METSIM (S), 3=FUSION, 4=TwinsUK, 5=GTEx (1=FUSION, 2=GTEx sex-stratified)
gene_N Gene sample size

Files

SuppTable10_FemaleOnly_eQTL_signals.txt

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