How to retrieve genes, score and betas for genes functionally implicated by a single variant
This tutorial shows how you can retrieve the overall score, beta coefficient values, p-values and other related statistics for all genes functionally implicated by a single variant (e.g. 11_59864062_C_T).
Use the genesForVariantquery:
{v_11_59864062_C_T: genesForVariant(variantId: "11_59864062_C_T") {overallScoregene {idsymbolchromosomestartendtss}qtls {aggregatedScoretypeIdsourceIdtissues {tissue {idname}quantilebetapval}}}}
Response
{"data": {"v_11_59864062_C_T": [{"overallScore": 0.04532967032967032,"gene": {"id": "ENSG00000254952","symbol": "AP001257.1","chromosome": "11","start": 60159687,"end": 60160822,"tss": 60160822},"qtls": []},{"overallScore": 0.03626373626373626,"gene": {"id": "ENSG00000110077","symbol": "MS4A6A","chromosome": "11","start": 60172014,"end": 60184666,"tss": 60184666},"qtls": []},{"overallScore": 0.009065934065934065,"gene": {"id": "ENSG00000166926","symbol": "MS4A6E","chromosome": "11","start": 60334831,"end": 60396596,"tss": 60334831},"qtls": []},{"overallScore": 0.01813186813186813,"gene": {"id": "ENSG00000172324","symbol": "OR5A2","chromosome": "11","start": 59416969,"end": 59426412,"tss": 59426412},"qtls": []},{"overallScore": 0.07252747252747252,"gene": {"id": "ENSG00000255393","symbol": "OOSP4B","chromosome": "11","start": 59978020,"end": 60031077,"tss": 59978020},"qtls": []},{"overallScore": 0.027197802197802195,"gene": {"id": "ENSG00000214787","symbol": "MS4A4E","chromosome": "11","start": 60200270,"end": 60243137,"tss": 60243137},"qtls": []},{"overallScore": 0.0815934065934066,"gene": {"id": "ENSG00000284873","symbol": "OOSP1","chromosome": "11","start": 59938432,"end": 59957480,"tss": 59938432},"qtls": []},{"overallScore": 0.01813186813186813,"gene": {"id": "ENSG00000172320","symbol": "OR5A1","chromosome": "11","start": 59436469,"end": 59451380,"tss": 59436469},"qtls": []},{"overallScore": 0.01813186813186813,"gene": {"id": "ENSG00000166884","symbol": "OR4D6","chromosome": "11","start": 59456938,"end": 59457991,"tss": 59456938},"qtls": []},{"overallScore": 0.027197802197802195,"gene": {"id": "ENSG00000254466","symbol": "OR4D10","chromosome": "11","start": 59473315,"end": 59479361,"tss": 59473315},"qtls": []},{"overallScore": 0.027197802197802195,"gene": {"id": "ENSG00000172742","symbol": "OR4D9","chromosome": "11","start": 59511368,"end": 59520703,"tss": 59511368},"qtls": []},{"overallScore": 0.0815934065934066,"gene": {"id": "ENSG00000166902","symbol": "MRPL16","chromosome": "11","start": 59806140,"end": 59810778,"tss": 59810778},"qtls": []},{"overallScore": 0.05439560439560439,"gene": {"id": "ENSG00000110048","symbol": "OSBP","chromosome": "11","start": 59574398,"end": 59615774,"tss": 59615774},"qtls": []},{"overallScore": 0.07252747252747252,"gene": {"id": "ENSG00000285010","symbol": "OOSP4A","chromosome": "11","start": 59964033,"end": 59970146,"tss": 59964033},"qtls": []},{"overallScore": 0.04532967032967032,"gene": {"id": "ENSG00000255008","symbol": "AP000442.1","chromosome": "11","start": 59561146,"end": 59566074,"tss": 59566074},"qtls": []},{"overallScore": 0.06346153846153844,"gene": {"id": "ENSG00000149516","symbol": "MS4A3","chromosome": "11","start": 60056587,"end": 60071115,"tss": 60056587},"qtls": []},{"overallScore": 0.05439560439560439,"gene": {"id": "ENSG00000149534","symbol": "MS4A2","chromosome": "11","start": 60088261,"end": 60098467,"tss": 60088261},"qtls": []},{"overallScore": 0.06346153846153844,"gene": {"id": "ENSG00000172289","symbol": "OR10V1","chromosome": "11","start": 59712916,"end": 59713845,"tss": 59713845},"qtls": []},{"overallScore": 0.09065934065934064,"gene": {"id": "ENSG00000134812","symbol": "CBLIF","chromosome": "11","start": 59829273,"end": 59845499,"tss": 59845499},"qtls": []},{"overallScore": 0.5802197802197802,"gene": {"id": "ENSG00000134827","symbol": "TCN1","chromosome": "11","start": 59852800,"end": 59866489,"tss": 59866489},"qtls": [{"aggregatedScore": 0.8,"typeId": "eqtl","sourceId": "eqtl","tissues": [{"tissue": {"id": "CEDAR-NEUTROPHIL_CD15","name": "Neutrophil cd15 (CEDAR)"},"quantile": 0.2,"beta": -0.340358,"pval": 0.00000317354},{"tissue": {"id": "eQTLGen-UBERON_0000178","name": "Blood (eQTLGen)"},"quantile": 0.8,"beta": -0.46303803943469946,"pval": 2.8499e-48},{"tissue": {"id": "Blueprint-NEUTROPHIL","name": "Neutrophil (Blueprint)"},"quantile": 0.3,"beta": -0.304993,"pval": 3.7648200000000005e-7}]},{"aggregatedScore": 0.9,"typeId": "pqtl","sourceId": "pqtl","tissues": [{"tissue": {"id": "SUN2018-UBERON_0001969","name": "Blood plasma (SUN2018)"},"quantile": 0.9,"beta": -0.7109,"pval": 4.570881896148752e-30}]}]},{"overallScore": 0.05439560439560439,"gene": {"id": "ENSG00000255139","symbol": "AP000442.2","chromosome": "11","start": 59616429,"end": 59639861,"tss": 59616429},"qtls": []},{"overallScore": 0.03626373626373626,"gene": {"id": "ENSG00000110079","symbol": "MS4A4A","chromosome": "11","start": 60185702,"end": 60317944,"tss": 60185702},"qtls": []},{"overallScore": 0.06346153846153844,"gene": {"id": "ENSG00000149507","symbol": "OOSP2","chromosome": "11","start": 60040409,"end": 60048044,"tss": 60040409},"qtls": []},{"overallScore": 0.06346153846153844,"gene": {"id": "ENSG00000166889","symbol": "PATL1","chromosome": "11","start": 59636716,"end": 59669037,"tss": 59669037},"qtls": []},{"overallScore": 0.027197802197802195,"gene": {"id": "ENSG00000176200","symbol": "OR4D11","chromosome": "11","start": 59503576,"end": 59504511,"tss": 59503576},"qtls": []},{"overallScore": 0.09065934065934064,"gene": {"id": "ENSG00000285231","symbol": "OOSP3","chromosome": "11","start": 59878809,"end": 59896481,"tss": 59878809},"qtls": []},{"overallScore": 0.06346153846153844,"gene": {"id": "ENSG00000166900","symbol": "STX3","chromosome": "11","start": 59713456,"end": 59805882,"tss": 59713456},"qtls": []}]}}
Last updated 7 months ago