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") {
overallScore
gene {
id
symbol
chromosome
start
end
tss
}
qtls {
aggregatedScore
typeId
sourceId
tissues {
tissue {
id
name
}
quantile
beta
pval
}
}
}
}

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": []
}
]
}
}
Retrieving genes, score and betas for genes implicated by a single variant using GraphiQL