| Title: | Data sources for genetic instruments to be used in MR |
|---|---|
| Description: | Datasets of eQTLs, GWAS catalogs, etc. |
| Authors: | Gibran Hemani [aut, cre] |
| Maintainer: | Gibran Hemani <[email protected]> |
| License: | CC0 |
| Version: | 0.3.2 |
| Built: | 2024-10-30 05:30:58 UTC |
| Source: | https://github.com/MRCIEU/MRInstruments |
mQTL analysis was performed in five time points in mothers and children. These data are obtained from http://www.gtexportal.org/home/ (GCTA version).
aries_mqtlaries_mqtl
A data frame with 187318 rows and 19 columns
SNP
timepoint
cpg
beta
pval
se
snp_chr
snp_pos
effect_allele
other_allele
eaf
sex
age
units
island_location
cpg_chr
cpg_pos
gene
gene_location
cis or trans acting mQTL
http://www.gtexportal.org/home/
Data was downloaded from ftp://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/qtl_as/QTL_RESULTS/mono_gene_nor_combat_peer_10_all_summary.txt.gz. Top hit SNPs filtered for (all associations with P<5e-8).
blueprint_monocyte_eqtlblueprint_monocyte_eqtl
A data frame with 452537 rows and 8 columns
Gene name
SNP rs ID
Effect size
Standard error
Effect allele frequency
Effect allele
Non effect allele
p-value
https://scmv-ieugit.epi.bris.ac.uk/gh13047/blueprint_monocyte_tophits
List of drug names and the genes that they target, along with information about how they interact and source of information
drug_interactionsdrug_interactions
A data frame with 38116 rows and 6 columns
entrez gene symbol
gene long name
interaction claim source
interaction types
drug name
drug primary name
The "Interactions TSV" at http://dgidb.genome.wustl.edu/downloads
The drug trial information comes from PMID 26121088 supplementary table 13. For a number of genes information is provided about diseases for which they are targeted, and the status of the trials in which they were tested.
gene_trialsgene_trials
A data frame with 19085 rows and 5 columns
Entrez Gene symbol
MeSH term 1
Top MeSH term
Phase of drug development
Approved in EU or US
http://www.ncbi.nlm.nih.gov/pubmed/26121088
Gene expression - SNP associations from 27094 gene names and 44 tissues. Obtained from http://www.gtexportal.org/home/.
These data only include associations that GTEx labelled as is_choson_snp.
gtex_eqtlgtex_eqtl
A data frame with 280630 rows and 11 columns
Gene name
Tissue
Gene chromosome : gene start position (b37)
SNP rs ID
SNP chromosome : SNP position (b37)
Effect allele
Non effect allele
Effect size
Standard error
p-value
samplesize
https://scmv-ieugit.epi.bris.ac.uk/gh13047/gtex_data
Downloaded from EBI on 18/03/2016. Standardised to make units as consistent as possible, trait names, obtain gene annotation. Effect sizes and standard errors are all converted to log odds ratio for binary traits. Ensembl used to identify alleles and effect allele frequency where missing.
gwas_cataloggwas_catalog
A data frame with 22783 rows and 17 columns
Simple phenotype name
This phenotype also has units and details if they are necessary to distinguish different studies
Phenotype_info
PubmedID
Author
Year
SNP
chr
bp_ens_GRCh38
Region
gene
Gene_ens
effect_allele
other_allele
beta
se
pval
units
eaf
Date GWAS catalog downloaded and added to MR-Base
Sample size and ancestry description for stage 1 of GWAS (summing across multiple Stage 1 populations, if applicable)
Sample size and ancestry description for subsequent replication(s) (summing across multiple populations, if applicable)
URI of the EFO trait
Mapped Experimental Factor Ontology trait for this study
Accession ID allocated to a GWAS Catalog study
https://scmv-ieugit.epi.bris.ac.uk/gh13047/gwas_catalog_standardisation
Data provided by Peter Wurtz and Mika Ala-Korpela ahead of publication
metab_qtlsmetab_qtls
A data frame with 1088 rows and 12 columns
phenotype
chromosome
position
SNP rs ID
Effect allele
Non effect allele
effect allele frequency
Effect size
Standard error
p-value
number of studies
samplesize
unpublished
Created from the MR-Base database 23/12/2017 The top hits (5e-8) are extracted from these files and then the 1kg European dataset is used to clump the top hits (rsq = 0.001, kb = 10000)
mrbase_instrumentsmrbase_instruments
A data frame with 29792 rows and 16 columns
This phenotype also has units and details if they are necessary to distinguish different studies
id.exposure
samplesize.exposure
ncase.exposure
ncontrol.exposure
mr_keep.exposure
pval_origin.exposure
data_source.exposure
SNP
effect_allele.exposure
other_allele.exposure
beta.exposure
se.exposure
pval.exposure
units.exposure
eaf.exposure
GWAS of immunoassays of 190 protein levels from plasma
proteomic_qtlsproteomic_qtls
A data frame with 56 rows and 13 columns
analyte
chr
position
SNP
gene
location
annotation
effect_allele
other_allele
eaf
MAF
pval
beta
se
https://scmv-ieugit.epi.bris.ac.uk/gh13047/proteomic_qtls