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Glossary

Column/Element Name

Description

NHLBIkey

Unique key for NHLBI GRASP db (concatenation of PMID with row # in database)

Snp_id_current

Latest snp ID from dbSNP, it can be different from the original SNP entry in the database due to SNPmerges (merged = 1)

Pvalue

P-value for SNP-phenotype association

Phenotype

Phenotype description of SNP-phenotype entry

PMID

PubMed identifier for paper from which the SNP association originates

LocationWithinPaper

Place where SNP-phenotype result is located within paper (e.g., specific Table, Figure, text or Supplemental text, or extracted from Full GWAS scan results or other web-posted files)

PaperPhenotypeCategories

Categories assigned by NHLBI to the overall phenotype(s) focus of the paper

chr(hg19)

Human genome build 19 chromosome location of SNP

pos(hg19)

Human genome build 19 chromosomal position of SNP

InGene

Is the SNP entry within a transcribed region of 1 or more RefSeq protein coding genes?

dbSNPMAF

What is the global minor allele frequency (GMAF) for the given allele in dbSNP

dbSNPalleles/het/se

Observed dbSNP alleles, overall het +/- s.e.

dbSNPvalidation

Does SNP have some level of validation in dbSNP?

dbSNPClinStatus

Has dbSNP annotated SNP for clinical relevance?

Functional_class

Functional class(es) for SNP provided via dbGaP

ORegAnno

Is the SNP within a literature-derived functional regulatory region (ORegAnno database)?

ConservPredTFBS

Cross-mammal conserved predicted transcription factor binding sites from Hidden Markov Models (z-scores >= 3.0)

HumanEnhancer

Is the SNP within a positively validated human enhancer region (from the VistaEnhancers dataset)?

RNAEdit

Is the SNP within an RNA editing site from the DARNED database?

InLincRNA

Is the SNP entry within a transcribed region of 1 or more long intergenic noncoding RNA?

InMiRNA

Is the SNP entry within a transcribed region of 1 or more microRNA?

InMiRNABS

Is the SNP within 1 or more predicted microRNA binding site(PolyMiRTS v.2)?

PolyPhen

Does the SNP have a prediction result in PolyPhen2? If so, what is the result?

SIFT

Does the SNP have a prediction result in SIFT? If so, what is the result?

UniProtAnnotation

Is the SNP within an annotated protein functional region from UniProtKB (e.g., post-translational modification protein site, enzyme active site)?

Omim_id

OMIM ID(s) for SNP

Snp_gene_symbols

Gene symbol from current dbSNP build, semi-colon separated list for a given np_id_current

Upstream_gene_symbol

Gene symbol that is left to snp_id_current from the table created from NCBI RefSeq genes at dbGaP group

Upstream_gene_distance

Distance for a snp_id_current to a left gene from the table created from NCBI RefSeq genes at dbGaP group

Downstream_gene_symbol

Gene symbol that is right to snp_id_current from the table created from NCBI RefSeq genes at dbGaP group

Downstream_gene_distance

Distance for a snp_id_current to a right gene from the table created from NCBI RefSeq genes at dbGaP group

Intergenic

Based on NCBI RefSeq genes at dbGaP group

  • 1: on a gene
  • 2: having left and right genes, or between genes
  • 3: no left gene
  • 4: no right gene

PaperPhenotypeDescription

Description of the overall phenotype(s) focus of the paper

DatePub

Date of publication (based on either PubMed, NHGRI catalog, or abstracted from paper PDF)

Initial Sample Description

Sample size and demographic description for initial stage/discovery GWAS

Replication Sample Description

Replication sample size and demographic description (NR = none reported)

Platform [SNPs passing QC]

Description of genotyping and/or imputation platform(s) and number of SNP markers (specified or approximated) included in post-QC analyses

GWASancestryDescription

Ethnodemographic description of the paper population(s) (e.g., European, Mixed)

TotalSamples(discovery+replication)

Total number of analyzed samples in discovery + replication phases

TotalDiscoverySamples

Total number of analyzed samples in discovery phase

Total replication samples

Total number of analyzed samples in replication phase

Journal

Journal where paper was published

Exclusively Male/Female

Does the paper include ONLY analyses that are gender-specific? (i.e., all GWAS and/or replication samples are a single gender)

IncludesMale/Female Only Analyses

Does the paper include either SOME or ALL analyses that are gender-specific? (i.e., GWAS and/or replication sample is all male or female)

LastCurationDate

Last date that this entry was modified

CreationDate

Date this entry was created in the database

Columns included in full database download ONLY:

HUPfield

NULL field for release date in Entrez

SNPid(dbSNP134)

The rsID in dbSNP build134 ("rs" not included)

SNPid(in paper)

The rsID or other variant identifier given in the original publication (often but not always equal to the current rsID)

Title

Manuscript title

(Multiple) Ancestry sample size columns

Sample size counts in discovery and replication for ancestry groups. Where blank assumed to be 0. "Mixed" indicates a mixture of ancestries was reported but the proportion in each group was unclear. "Unspecified" means no ancestry was clearly specified for samples

EqtlMethMetabStudy

Indicates if a result is from an eQTL, methylation QTL or metabolomics GWAS (1=yes) and thus not included in web interface queries