"Thsi element represents the tag variant with its associated statistics" type CredSetTagElement { "Tag Variant in the credibleset table" tagVariant: Variant! "p-val" pval: Float! "SE" se: Float! "beta" beta: Float! "Posterior Probability" postProb: Float! "Multisignal Method" MultisignalMethod: String! "Log ABF" logABF: Float! "Is over 95 percentile" is95: Boolean! "Is over 99 percentile" is99: Boolean! } "A list of rows with each link" type DistanceElement { typeId: String! sourceId: String! aggregatedScore: Float! tissues: [DistanceTissue!]! } type DistanceTissue { tissue: Tissue! "Distance to the canonical TSS" distance: Long "Score 1 / Distance" score: Float "Quantile of the score" quantile: Float } type FPredTissue { tissue: Tissue! maxEffectLabel: String maxEffectScore: Float } "A list of rows with each link" type FunctionalPredictionElement { typeId: String! sourceId: String! aggregatedScore: Float! tissues: [FPredTissue!]! } "A list of rows with each link" type G2VSchema { "qtl structure definition" qtls: [G2VSchemaElement!]! "qtl structure definition" intervals: [G2VSchemaElement!]! "qtl structure definition" functionalPredictions: [G2VSchemaElement!]! "Distance structure definition" distances: [G2VSchemaElement!]! } "A list of rows with each link" type G2VSchemaElement { id: String! sourceId: String! sourceLabel: String sourceDescriptionOverview: String sourceDescriptionBreakdown: String "PubmedID" pmid: String tissues: [Tissue!]! } type GWASColocalisation { "Tag variant ID as ex. 1_12345_A_T" indexVariant: Variant! "study ID" study: Study! "Beta" beta: Float "H3" h3: Float! "H4" h4: Float! "Log2 H4/H3" log2h4h3: Float! } type GWASColocalisationForQTLWithGene { "Tag variant ID as ex. 1_12345_A_T" leftVariant: Variant! "GWAS Study" study: Study! "QTL study ID" qtlStudyId: String! "Phenotype ID" phenotypeId: String! "QTL bio-feature" tissue: Tissue! "H3" h3: Float! "H4" h4: Float! "Log2 H4/H3" log2h4h3: Float! } type GWASLRColocalisation { "Tag variant ID as ex. 1_12345_A_T" leftVariant: Variant! "study ID" leftStudy: Study! "Tag variant ID as ex. 1_12345_A_T" rightVariant: Variant! "study ID" rightStudy: Study! "H3" h3: Float! "H4" h4: Float! "Log2 H4/H3" log2h4h3: Float! } type Gecko { genes: [Gene!]! tagVariants: [Variant!]! indexVariants: [Variant!]! studies: [Study!]! geneTagVariants: [GeneTagVariant!]! tagVariantIndexVariantStudies: [TagVariantIndexVariantStudy!]! } "This element represents a simple gene object which contains id and name" type Gene { "Ensembl Gene ID of a gene" id: String! "Approved symbol name of a gene" symbol: String "Description of a gene" description: String "Chromosome" chromosome: String "Start position for the gene" start: Long "End position for the gene" end: Long "Transcription start site" tss: Long "Bio-type of the gene" bioType: String "Forward strand true or false" fwdStrand: Boolean "Approved symbol name of a gene" exons: [Long!]! } "A list of rows with each link" type GeneForVariant { "Associated scored gene" gene: Gene! "Associated scored variant" variant: String! overallScore: Float! qtls: [QTLElement!]! intervals: [IntervalElement!]! functionalPredictions: [FunctionalPredictionElement!]! distances: [DistanceElement!]! } type GeneTagVariant { geneId: String! tagVariantId: String! overallScore: Float } "This object represent a link between a triple (study, trait, index_variant) and a tag variant via an expansion method (either ldExpansion or FineMapping)" type IndexVariantAssociation { "Tag variant ID as ex. 1_12345_A_T" tagVariant: Variant! "study ID" study: Study! "p-val between a study and an the provided index variant" pval: Float! "p-val between a study and an the provided index variant" pvalMantissa: Float! "p-val between a study and an the provided index variant" pvalExponent: Long! "n total cases (n initial + n replication)" nTotal: Long! "n cases" nCases: Long! "study ID" overallR2: Float afr1000GProp: Float amr1000GProp: Float eas1000GProp: Float eur1000GProp: Float sas1000GProp: Float log10Abf: Float posteriorProbability: Float oddsRatio: Float oddsRatioCILower: Float oddsRatioCIUpper: Float beta: Float betaCILower: Float betaCIUpper: Float direction: String } "A list of rows with each link" type IndexVariantsAndStudiesForTagVariant { "A list of associations connected to a Index variant and a Study through some expansion methods" associations: [TagVariantAssociation!]! } "A list of rows with each link" type IntervalElement { typeId: String! sourceId: String! aggregatedScore: Float! tissues: [IntervalTissue!]! } type IntervalTissue { tissue: Tissue! quantile: Float! score: Float } "This element represents a Manhattan like plot" type Manhattan { "A list of associations" associations: [ManhattanAssociation!]! "A list of overlapped studies" topOverlappedStudies( "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): TopOverlappedStudies } "This element represents an association between a trait and a variant through a study" type ManhattanAssociation { "Index variant" variant: Variant! "Computed p-Value" pval: Float! "p-val between a study and an the provided index variant" pvalMantissa: Float! "p-val between a study and an the provided index variant" pvalExponent: Long! oddsRatio: Float oddsRatioCILower: Float oddsRatioCIUpper: Float beta: Float betaCILower: Float betaCIUpper: Float direction: String "A list of best genes associated" bestGenes: [ScoredGene!]! "A list of best genes associated" bestColocGenes: [ScoredGene!]! "A list of best L2G scored genes associated" bestLocus2Genes: [ScoredGene!]! "The cardinal of the set defined as tag variants for an index variant coming from crediblesets" credibleSetSize: Long "The cardinal of the set defined as tag variants for an index variant coming from ld expansion" ldSetSize: Long "The cardinal of the set defined as tag variants for an index variant coming from any expansion" totalSetSize: Long! } "This element represent an overlap between two variants for two studies" type Overlap { variantIdA: String! variantIdB: String! overlapAB: Long! distinctA: Long! distinctB: Long! } type OverlappedInfoForStudy { "A study object" study: Study overlappedVariantsForStudies: [OverlappedVariantsStudies!]! variantIntersectionSet: [String!]! } "This element represent a overlap between two stduies" type OverlappedStudy { "A study object" study: Study! "Orig variant id which is been used for computing the overlap with the referenced study" numOverlapLoci: Int! } "This element represent a overlap between two stduies" type OverlappedVariantsStudies { "A study object" study: Study "Orig variant id which is been used for computing the overlap with the referenced study" overlaps: [Overlap!]! } "This element represents a PheWAS like plot" type PheWAS { "A total number of unique GWAS studies in the summary stats table" totalGWASStudies: Long! "A list of associations" associations: [PheWASAssociation!]! } "This element represents an association between a variant and a reported trait through a study" type PheWASAssociation { "Study Object" study: Study "Computed p-Value" pval: Float! "beta" beta: Float "total sample size (variant level)" nTotal: Long "number of cases" nCases: Long "Odds ratio (if case control)" oddsRatio: Float "Effect Allele Frequency" eaf: Float "Standard Error" se: Float } type QTLColocalisation { "Tag variant ID as ex. 1_12345_A_T" indexVariant: Variant! "Gene" gene: Gene! "QTL Phenotype ID" phenotypeId: String! "QTL bio-feature" tissue: Tissue! "QTL study ID" qtlStudyName: String! "Beta" beta: Float "H3" h3: Float! "H4" h4: Float! "Log2 H4/H3" log2h4h3: Float! } "A list of rows with each link" type QTLElement { typeId: String! sourceId: String! aggregatedScore: Float! tissues: [QTLTissue!]! } type QTLTissue { tissue: Tissue! quantile: Float! beta: Float pval: Float } type Query { search( "Query text to search for" queryString: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): SearchResult! genes( "Chromosome as String between 1..22 or X, Y, MT" chromosome: String!, "Start position in a specified chromosome" start: Long!, "End position in a specified chromosome" end: Long!): [Gene!]! geneInfo( "Gene ID using Ensembl identifier" geneId: String!): Gene studyInfo( "Study ID which links a top loci with a trait" studyId: String!): Study variantInfo( "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!): Variant studiesForGene( "Gene ID using Ensembl identifier" geneId: String!): [StudyForGene!]! studyLocus2GeneTable( "Study ID which links a top loci with a trait" studyId: String!, "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): SLGTable! manhattan( "Study ID which links a top loci with a trait" studyId: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): Manhattan! topOverlappedStudies( "Study ID which links a top loci with a trait" studyId: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): TopOverlappedStudies! overlapInfoForStudy( "Study ID which links a top loci with a trait" studyId: String!, "List of study IDs" studyIds: [String!]!): OverlappedInfoForStudy! tagVariantsAndStudiesForIndexVariant( "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): TagVariantsAndStudiesForIndexVariant! indexVariantsAndStudiesForTagVariant( "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): IndexVariantsAndStudiesForTagVariant! pheWAS( "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): PheWAS! gecko( "Chromosome as String between 1..22 or X, Y, MT" chromosome: String!, "Start position in a specified chromosome" start: Long!, "End position in a specified chromosome" end: Long!): Gecko genesForVariantSchema: G2VSchema! genesForVariant( "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!): [GeneForVariant!]! gwasRegional( "Study ID which links a top loci with a trait" studyId: String!, "Chromosome as String between 1..22 or X, Y, MT" chromosome: String!, "Start position in a specified chromosome" start: Long!, "End position in a specified chromosome" end: Long!): [RegionalAssociation!]! qtlRegional( "Study ID which links a top loci with a trait" studyId: String!, "BioFeature represents either a tissue, cell type, aggregation type, ..." bioFeature: String!, "Phenotype ID using Ensembl identifier for the molecular traits" phenotypeId: String!, "Chromosome as String between 1..22 or X, Y, MT" chromosome: String!, "Start position in a specified chromosome" start: Long!, "End position in a specified chromosome" end: Long!): [RegionalAssociation!]! studyAndLeadVariantInfo( "Study ID which links a top loci with a trait" studyId: String!, "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!): StudiesAndLeadVariantsForGene gwasCredibleSet( "Study ID which links a top loci with a trait" studyId: String!, "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!): [CredSetTagElement!]! qtlCredibleSet( "Study ID which links a top loci with a trait" studyId: String!, "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!, "Phenotype ID using Ensembl identifier for the molecular traits" phenotypeId: String!, "BioFeature represents either a tissue, cell type, aggregation type, ..." bioFeature: String!): [CredSetTagElement!]! colocalisationsForGene( "Gene ID using Ensembl identifier" geneId: String!): [GWASColocalisationForQTLWithGene!]! gwasColocalisationForRegion( "Chromosome as String between 1..22 or X, Y, MT" chromosome: String!, "Start position in a specified chromosome" start: Long!, "End position in a specified chromosome" end: Long!): [GWASLRColocalisation!]! gwasColocalisation( "Study ID which links a top loci with a trait" studyId: String!, "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!): [GWASColocalisation!]! qtlColocalisation( "Study ID which links a top loci with a trait" studyId: String!, "Variant ID formated as CHR_POSITION_REFALLELE_ALT_ALLELE" variantId: String!): [QTLColocalisation!]! studiesAndLeadVariantsForGene( "Gene ID using Ensembl identifier" geneId: String!): [StudiesAndLeadVariantsForGene!]! studiesAndLeadVariantsForGeneByL2G( "Gene ID using Ensembl identifier" geneId: String!, "pagination index >= 0" pageIndex: Int, "pagination size > 0" pageSize: Int): [V2DL2GRowByGene!]! } "Variant with a p-val" type RegionalAssociation { "Summary Stats simple variant information" variant: Variant! "p-val" pval: Float! } type SLGRow { yProbaDistance: Float! yProbaInteraction: Float! yProbaMolecularQTL: Float! yProbaPathogenicity: Float! yProbaModel: Float! hasColoc: Boolean! distanceToLocus: Long! "Gene" gene: Gene! } type SLGTable { rows: [SLGRow!]! "Study" study: Study "Variant" variant: Variant } "This object link a Gene with a score" type ScoredGene { "Gene Info" gene: Gene! "Score a Float number between [0. .. 1.]" score: Float! } "Search data by a query string" type SearchResult { "Total number of genes found" totalGenes: Long! "Total number of variants found" totalVariants: Long! "Total number of studies found" totalStudies: Long! "Gene search result list" genes: [Gene!]! "Variant search result list" variants: [Variant!]! "Study search result list" studies: [Study!]! } "A list of Studies and Lead Variants for a Gene" type StudiesAndLeadVariantsForGene { "Tag variant ID as ex. 1_12345_A_T" indexVariant: Variant! "study ID" study: Study! "p-val between a study and an the provided index variant" pval: Float! "p-val between a study and an the provided index variant" pvalMantissa: Float! "p-val between a study and an the provided index variant" pvalExponent: Long! oddsRatio: Float oddsRatioCILower: Float oddsRatioCIUpper: Float beta: Float betaCILower: Float betaCIUpper: Float direction: String } "This element contains all study fields" type Study { "Study Identifier" studyId: String! "Trait Label as reported on the publication" traitReported: String! "A list of curated efo codes" traitEfos: [String!]! "PubMed ID for the corresponding publication" pmid: String "Publication Date as YYYY-MM-DD" pubDate: String "Publication Journal name" pubJournal: String "Publication Title" pubTitle: String "Publication author" pubAuthor: String "Contains summary stats info" hasSumsStats: Boolean "Ancestry initial" ancestryInitial: [String!]! "Ancestry replication" ancestryReplication: [String!]! "N initial" nInitial: Long "N replication" nReplication: Long "N cases" nCases: Long "n total cases (n initial + n replication)" nTotal: Long! "Trait category" traitCategory: String "Number of associated loci" numAssocLoci: Long } type StudyForGene { "A study object" study: Study! } "This object represent a link between a triple (study, trait, index_variant) and a tag variant via an expansion method (either ldExpansion or FineMapping)" type TagVariantAssociation { "Tag variant ID as ex. 1_12345_A_T" indexVariant: Variant! "study ID" study: Study! "p-val between a study and an the provided index variant" pval: Float! "p-val between a study and an the provided index variant" pvalMantissa: Float! "p-val between a study and an the provided index variant" pvalExponent: Long! "n total cases (n initial + n replication)" nTotal: Long! "n cases" nCases: Long! "study ID" overallR2: Float afr1000GProp: Float amr1000GProp: Float eas1000GProp: Float eur1000GProp: Float sas1000GProp: Float log10Abf: Float posteriorProbability: Float oddsRatio: Float oddsRatioCILower: Float oddsRatioCIUpper: Float beta: Float betaCILower: Float betaCIUpper: Float direction: String } type TagVariantIndexVariantStudy { tagVariantId: String! indexVariantId: String! studyId: String! r2: Float posteriorProbability: Float pval: Float! "p-val between a study and an the provided index variant" pvalMantissa: Float! "p-val between a study and an the provided index variant" pvalExponent: Long! oddsRatio: Float oddsRatioCILower: Float oddsRatioCIUpper: Float beta: Float betaCILower: Float betaCIUpper: Float direction: String } "A list of rows with each link" type TagVariantsAndStudiesForIndexVariant { "A list of associations connected to a Index variant and a Study through some expansion methods" associations: [IndexVariantAssociation!]! } type Tissue { id: String! name: String! } "This element represent a overlap between two stduies" type TopOverlappedStudies { "A study object" study: Study "Top N studies ordered by loci overlap" topStudiesByLociOverlap: [OverlappedStudy!]! } type V2DBeta { direction: String betaCI: Float betaCILower: Float betaCIUpper: Float } type V2DL2GRowByGene { odds: V2DOdds! beta: V2DBeta! pval: Float! pvalExponent: Long! pvalMantissa: Float! yProbaDistance: Float! yProbaInteraction: Float! yProbaMolecularQTL: Float! yProbaPathogenicity: Float! yProbaModel: Float! "Study" study: Study! "Variant" variant: Variant! } type V2DOdds { oddsCI: Float oddsCILower: Float oddsCIUpper: Float } "This element represents a variant object" type Variant { "Variant ID" id: String! "Variant ID GRCH37" idB37: String "Approved symbol name of a gene" rsId: String "Ensembl Gene ID of a gene" chromosome: String! "Approved symbol name of a gene" position: Long! "chrom id GRCH37" chromosomeB37: String "Approved symbol name of a gene" positionB37: Long "Ref allele" refAllele: String! "Alt allele" altAllele: String! "Nearest gene" nearestGene: Gene "Distance to the nearest gene (any biotype)" nearestGeneDistance: Long "Nearest protein-coding gene" nearestCodingGene: Gene "Distance to the nearest gene (protein-coding biotype)" nearestCodingGeneDistance: Long "Most severe consequence" mostSevereConsequence: String "Combined Annotation Dependent Depletion - Raw score" caddRaw: Float "Combined Annotation Dependent Depletion - Scaled score" caddPhred: Float "gnomAD Allele frequency (African/African-American population)" gnomadAFR: Float "gnomAD Allele frequency (Latino/Admixed American population)" gnomadAMR: Float "gnomAD Allele frequency (Ashkenazi Jewish population)" gnomadASJ: Float "gnomAD Allele frequency (East Asian population)" gnomadEAS: Float "gnomAD Allele frequency (Finnish population)" gnomadFIN: Float "gnomAD Allele frequency (Non-Finnish European population)" gnomadNFE: Float "gnomAD Allele frequency (Non-Finnish Eurpoean Estonian sub-population)" gnomadNFEEST: Float "gnomAD Allele frequency (Non-Finnish Eurpoean North-Western European sub-population)" gnomadNFENWE: Float "gnomAD Allele frequency (Non-Finnish Eurpoean Southern European sub-population)" gnomadNFESEU: Float "gnomAD Allele frequency (Non-Finnish Eurpoean Other non-Finnish European sub-population)" gnomadNFEONF: Float "gnomAD Allele frequency (Other (population not assigned) population)" gnomadOTH: Float }