Table Columns

The two important tables with the majority of the data are Study and SNP. In addition, phenotype data is stored in Phenotype and PhenoCats, population data is in Population, and platforms are in Platform.

Study

To query studies, it is recommended to use the query.get_studies() function.

Column Description Type
id id Integer
pmid PubmedID String
title Study String
journal Journal String
author 1st_author String
grasp_ver GRASPversion? Integer
noresults No results flag Boolean
results #results Integer
qtl IsEqtl/meQTL/pQTL/gQTL/Metabolmics? Boolean
snps Link to all SNPs in this study relationship
phenotype_id ID of primary phenotype in Phenotype table Integer
phenotype A link to the primary phenotype in the Phenotype table relationship
phenotype_cats A link to all phenotype categories assigned in the PhenoCats table relationship
datepub DatePub Date
in_nhgri In NHGRI GWAS catalog (8/26/14)? Boolean
locations Specific place(s) mentioned for samples String
mf Includes male/female only analyses in discovery and/or replication? Boolean
mf_only Exclusively male or female study? Boolean
platforms Link to platforms in the Platform table. Platform [SNPs passing QC] relationship
snp_count From “Platform [SNPs passing QC]” String
imputed From “Platform [SNPs passing QC]” Boolean
population_id Primary key of population table Integer
population GWAS description, link to table relationship
total Total Discovery + Replication sample size Integer
total_disc Total discovery samples Integer
disc_pop_flag A bitwise flag that shows presence/absence of discovery populations Integer
european European Integer
african African ancestry Integer
east_asian East Asian Integer
south_asian Indian/South Asian Integer
hispanic Hispanic Integer
native Native Integer
micronesian Micronesian Integer
arab Arab/ME Integer
mixed Mixed Integer
unpecified Unspec Integer
filipino Filipino Integer
indonesian Indonesian Integer
total_rep Total replication samples Integer
rep_pop_flag A bitwise flag that shows presence/absence of replication populations Integer
rep_european European.1 Integer
rep_african African ancestry.1 Integer
rep_east_asian East Asian.1 Integer
rep_south_asian Indian/South Asian.1 Integer
rep_hispanic Hispanic.1 Integer
rep_native Native.1 Integer
rep_micronesian Micronesian.1 Integer
rep_arab Arab/ME.1 Integer
rep_mixed Mixed.1 Integer
rep_unpecified Unspec.1 Integer
rep_filipino Filipino.1 Integer
rep_indonesian Indonesian.1 Integer
sample_size Initial Sample Size, string description of integer population counts above. String
replication_size Replication Sample Size, string description of integer population counts above. String

SNP

Column Description Type
id NHLBIkey BigInteger
snpid SNPid String
chrom chr String
pos pos Integer
pval Pvalue Float
NHLBIkey NHLBIkey String
HUPfield HUPfield String
LastCurationDate LastCurationDate Date
CreationDate CreationDate Date
population_id Primary Integer
population Link relationship
study_id Primary Integer
study Link relationship
study_snpid SNPid String
paper_loc LocationWithinPaper String
phenotype_desc Phenotype String
phenotype_cats Link relationship
InGene InGene String
NearestGene NearestGene String
InLincRNA InLincRNA String
InMiRNA InMiRNA String
InMiRNABS InMiRNABS String
dbSNPfxn dbSNPfxn String
dbSNPMAF dbSNPMAF String
dbSNPinfo dbSNPalleles String
dbSNPvalidation dbSNPvalidation String
dbSNPClinStatus dbSNPClinStatus String
ORegAnno ORegAnno String
ConservPredTFBS ConservPredTFBS String
HumanEnhancer HumanEnhancer String
RNAedit RNAedit String
PolyPhen2 PolyPhen2 String
SIFT SIFT String
LSSNP LS String
UniProt UniProt String
EqtlMethMetabStudy EqtlMethMetabStudy String

Phenotype

All available phenotypes are available on the Phenotypes wiki page

  • id
  • phenotype
  • studies (link to Study table)
  • snps (link to SNP table)

PhenoCats

All phenotype categories are available on the Phenotype Categories wiki page

  • id
  • population
  • alias
  • studies (link to Study table)
  • snps (link to SNP table)

Population

  • id
  • population
  • studies (link to Study table)
  • snps (link to SNP table)

All population entries are available on the Populations wiki page

Platform

  • id
  • platform
  • studies (link to Study table)
  • snps (link to SNP table)