eQTL Catalogue Summary Statistics API Documentation

Overview

HTTP Verbs

This API supports the following HTTP verbs.

Verb	Usage
`GET`	Used to retrieve a resource

HTTP status codes

This API tries to adhere as closely as possible to standard HTTP and REST conventions in its use of HTTP status codes.

Status code	Usage
`200 OK`	The request completed successfully
`400 Bad Request`	The request was malformed. The response body will include an error providing further information
`404 Not Found`	The requested resource did not exist

Errors

Whenever an error response (status code >= 400) is returned, the body will contain a JSON object that describes the problem. The error object has the following structure:

Path	Type	Description
error	String	The HTTP error that occurred, e.g. `Bad Request`
message	String	A description of the cause of the error
status	Number	The HTTP status code, e.g. `400`

Hypermedia

This API uses hypermedia and resources include links to other resources in their responses. Responses are in Hypertext Application Language (HAL) format. Links can be found beneath the _links key. Users of the API should not created URIs themselves, instead they should use the above-described links to navigate from resource to resource.

API quick reference

With the exception of genomic region requests, all requests for associations can all be made using the /associations endpoint, adding and combining parameters as needed for filtering.

Resource	Operation	Description
Associations	GET /eqtl/api/associations	Lists all of the available associations.
Chromosome Resource	GET /eqtl/api/chromosomes/(string:chromosome)	List a specific chromosome resource
Chromosomes	GET /eqtl/api/chromosomes	List all chromosome resources
Gene Resource	GET /eqtl/api/genes/(string:gene_id)	Lists a specific gene resource.
Genes	GET /eqtl/api/genes	List all existing gene resources
Molecular Phenotype Resource	GET /eqtl/api/molecular_phenotypes/(string:molecular_trait_id)	Lists a specific molecular phenotype resource.
Molecular phenotypes	GET /eqtl/api/molecular_phenotypes	List all existing molecular phenotypes resources
QTL groups	GET /eqtl/api/qtl_groups	List all existing qtl groups (datasets)
Search Chromosome Associations	GET /eqtl/api/chromosomes/(string:chromosome)/associations	Returns associations for a specific chromosome. Will return 404 Not Found if the chromosome value does not exist.
Search Gene for Associations	GET /eqtl/api/genes/(string:gene_id)/associations	Lists associations for a specific gene id.
Search Molecular phenotype for Associations	GET /eqtl/api/molecular_phenotypes/(string:molecular_trait_id)/associations	Lists associations for a specific molecular trait id.
Search Study for Associations	GET /eqtl/api/tissues/(string:tissue)/studies/(string:study)/associations	Lists associations for a specific study.
	GET /eqtl/api/studies/(study)/associations
Search Tissue/Cell type for Associations	GET /eqtl/api/tissues/(string:tissue)/associations	Lists associations for a specific tissue ontology.
Search Variant on Chromosome	GET /eqtl/api/chromosomes/(string:chromosome)/associations/(string:variant_id)	Lists all of the available associations of a specific variant.
Studies	GET /eqtl/api/studies	List all existing study resources
Studies for tissues	GET /eqtl/api/tissues/(string:tissue)/studies	List all existing study resources for a given tissue ontology
Study	GET /eqtl/api/tissues/(string:tissue)/studies/(string:study)	Lists a specific study resource
	GET /eqtl/api/studies/(string:study)
Tissue	GET /eqtl/api/tissues/(string:tissue)	Lists a specific tissue/cell type ontology resource
Tissues	GET /eqtl/api/tissues	List all existing tissue/cell type resources
Variant Associations	GET /eqtl/api/associations/(string:rsid)	Lists all of the available associations of a specific variant.
	GET /eqtl/api/associations/(string:variant_id)

API General Guidelines

Association Queries

For all endpoints that return associations you can assume the below.

Default data values displayed are from the ‘ge’ (gene counts) quantification method. You can query specifically for any other quantification method choosing from the table below:

Quantification method	Reference
Gene counts	‘ge’
Exon counts	‘exon’
Microarray	‘microarray’
Transcript usage	‘tx’
Txrevise	‘txrevise’

Use the reference to specify the quantification method. For instance, if you want to view exon count data use the query parameter quant_method=exon. By default quant_method is set to ‘ge’. It is not possible to view all the quantification methods in one API call.

Depending on the endpoint, you can filter by the following parameters:

Parameter	Label	Example
Molecular trait	‘molecular_trait_id’	`molecular_trait_id=ENSG00000187583`
Gene	‘gene_id’	`gene_id=ENSG00000073067`
Variant	‘variant_id’	`variant_id=rs577290214`
Study	‘study’	`study=Alasoo_2018`
Tissue ontology	‘tissue’	`tissue=CL_0000235`
QTL group/context	‘qtl_group’	`qtl_group=macrophage_IFNg`

The above parameters can be applied to any endpoint that does not already search/filter by that parameter, e.g. the molecular trait parameter is ignored when applied to the molecular phenotypes endpoint. The parameters can be combined using the & operator to filter the data as much as needed but any single parameter can only be called once i.e. it is not possible to filter for multiple genes, for that you must make separate queries. In the case a combination of tissue and qtl_group, any QTL group will supersede the tissue filter, effectively nullifying the tissue filter. This is because a QTL context refers to a tissue and condition e.g. if the tissue/cell type is ‘macrophage’ and the condition/treatment is ‘Salmonella’, the corresponding QTL group is ‘macrophage_Salmonella’.

You can also filter all of the association endpoints by p-value. This is done by setting either the lower p-value threshold that you want to be cutoff, the upper p-value threshold that you want to be cutoff, or both. This is done by passing the query parameters p_lower=<lower p-value> and/or p_upper=<upper p-value> to the API call.

Furthermore, if you would like to query associations by a base-pair location range on a specific chromosome, you can pass in one or both of the following parameters, bp_lower=<lower base-pair limit> and bp_upper=<upper base-pair limit>. Note: base-pair location limit filtering will only work via the /chromosomes/(int: chromosome)/associations endpoint.

Response format

The links parameter, links, switches toggles whether to return URLs for that specific association, tissue, variant and study. The links are by default deactivated to improve performance and cannot be combined with the paginate=False parameter. The paginate parameter, paginate, allows you to flag whether the response should be paginated (using the size and start parameters) or not. By default it is set to ‘True’, but if set to ‘False’ the size and start parameters are ignored and the response will contain every hit. When using the un-paginated format none of the links seen in the paginated format will be present. Note that paginate=False can only be used on sufficiently filtered payloads (to avoid transmitting huge payloads). A sufficiently filtered request adheres to the following: study & qtl_group & (gene_id or molecular_trait_id or variant_id) i.e. requests for genes, molecular traits or variants for a specific study and QTL group can be returned as one single payload rather than paged responses.

Requesting associations for variant

You can query the associations of a specific variant by variant id or rsID. This can be done either via the /associations/(string: variant_id) or /associations/(string: rsid) endpoint, or it can be done as a parameter query like /associations/?variant_id=(string: variant_id/rsid).

Available data fields

Name	Type	Description
variant	String	The variant ID (CHR_BP_REF_ALT) e.g. chr19_226776_C_T
rsid	String	The rsID, if given, for the variant
chromosome	Number	GRCh38 chromosome name of the variant
position	Number	GRCh38 position of the variant
study_id	String	The study identifier e.g. Alasoo_2018
molecular_trait_id	String	ID of the molecular trait e.g. ENSG00000156508
pvalue	Number	P-value of association between the variant and the phenotype
neg_log10_pvalue	Number	Negative log10 p-value
ac	Number	Allele count
alt	String	GRCh38 effect allele (alt allele)
ref	String	GRCh38 other allele (reference allele)
maf	Number	Minor allele frequency within the QTL mapping study
median_tpm	Number	Expression value for the associated gene + qtl_group
type	String	SNP, INDEL or OTHER
an	Number	Total number of alleles
beta	Number	Regression coefficient from the linear model
gene_id	String	Ensembl gene ID
r2	Number	Imputation quality score from the imputation software
qtl_group	String	Controlled vocabulary for the QTL group (tissue & condition)
tissue	String	Ontology term for the tissue/cell type
tissue_label	String	Controlled vocabulary for the tissue/cell type
condition	String	Controlled vocabulary for the condition/treatment
condition_label	String	More verbose condition description

Listing Resources

Requests that return multiple resources will be paginated to 20 items by default. You can change number of items returned using the size parameter. The maximum size value is 1000 and any value given greater than 1000 will be converted to 1000.

Paging resources

Links will be provided in the response to navigate the resources.

Example request:

GET /associations?size=1 HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "associations": {
      "0": {
        "alt": "G",
        "condition": "naive",
        "rsid": "rs200141179",
        "condition_label": "naive",
        "ac": 240,
        "position": 230130,
        "chromosome": "19",
        "an": 972,
        "qtl_group": "brain",
        "beta": -0.0529243,
        "r2": 0.48226,
        "variant": "chr19_230130_GATC_G",
        "study_id": "BrainSeq",
        "ref": "GATC",
        "tissue_label": "brain",
        "type": "INDEL",
        "maf": 0.246914,
        "median_tpm": 12.272,
        "pvalue": 0.0166984,
        "neg_log10_pvalue": 1.77732514,
        "molecular_trait_id": "ENSG00000011304",
        "gene_id": "ENSG00000011304",
        "tissue": "UBERON_0009834",
      }
    }
  },
  "_links": {
    "self": {
      "href": "https://www.ebi.ac.uk/eqtl/api/associations"
    },
    "first": {
      "href": "https://www.ebi.ac.uk/eqtl/api/associations?size=1&start=0"
    },
    "next": {
      "href": "https://www.ebi.ac.uk/eqtl/api/associations?size=1&start=1"
    }
  }
}

Response structure

Path	Type	Description
_links	Object	Links to other resources
_embedded	Object	The list of resources

Links

Relation	Description
self	This resource list
first	The first page in the resource list
next	The next page in the resource list

When paging through results, the next link should always be used, and incrementing the search start parameter based on the size should be avoided. If you would like to return an un-paginated payload containing all the results, see Response format.

Accessing the API

The api endpoint provides the entry point into the service.

A GET request is used to access the API.

Example request:

GET / HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_links": {
    "associations": {
          "href": "https://www.ebi.ac.uk/eqtl/api/associations"
    },
    "molecular_phenotypes": {
          "href": "https://www.ebi.ac.uk/eqtl/api/molecular_phenotypes"
    },
    "studies": {
          "href": "https://www.ebi.ac.uk/eqtl/api/studies"
    },
    "tissues": {
          "href": "https://www.ebi.ac.uk/eqtl/api/tissues"
    },
    "genes": {
          "href": "https://www.ebi.ac.uk/eqtl/api/genes"
    },
    "chromosomes": {
          "href": "https://www.ebi.ac.uk/eqtl/api/chromosomes"
    }
  }
}

Response structure

Path	Type	Description
_links	Object	Links to other resources

Links

Relation	Description
associations	Link to the association resources in the database
molecular_phenotypes	Link to the molecular phenotypes resources in the database
studies	Link to the study resources in the database
tissues	Link to the tissue resources in the database
genes	Link to the gene resources in the database
chromosomes	Link to the chromosome resources in the database

API detailed reference

GET /eqtl/api/associations

Associations

Lists all of the available associations that are loaded into the database. Can be specify by p-value cutoff threshold.

Example request:

GET /associations HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "associations": {
      "0": {
        "alt": "G",
        "condition": "naive",
        "rsid": "rs200141179",
        "condition_label": "naive",
        "ac": 240,
        "position": 230130,
        "chromosome": "19",
        "an": 972,
        "qtl_group": "brain",
        "beta": -0.0529243,
        "r2": 0.48226,
        "variant": "chr19_230130_GATC_G",
        "study_id": "BrainSeq",
        "ref": "GATC",
        "tissue_label": "brain",
        "type": "INDEL",
        "maf": 0.246914,
        "median_tpm": 12.272,
        "pvalue": 0.0166984,
        "neg_log10_p_value": 1.77732514,
        "molecular_trait_id": "ENSG00000011304",
        "gene_id": "ENSG00000011304",
        "tissue": "UBERON_0009834",
      },
      "1": {
        "alt": "G",
        "condition": "naive",
        "rsid": "rs200141179",
        "condition_label": "naive",
        "ac": 240,
        "position": 230130,
        "chromosome": "19",
        "an": 972,
        "qtl_group": "brain",
        "beta": 0.0340718,
        "r2": 0.48226,
        "variant": "chr19_230130_GATC_G",
        "study_id": "BrainSeq",
        "ref": "GATC",
        "tissue_label": "brain",
        "type": "INDEL",
        "maf": 0.246914,
        "median_tpm": 27.623,
        "pvalue": 0.424836,
        "neg_log10_p_value": 0.371778689,
        "molecular_trait_id": "ENSG00000129951",
        "gene_id": "ENSG00000129951",
        "tissue": "UBERON_0009834",
      }
    }
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/associations"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/associations?start=0&size=2"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/associations?start=2&size=2"
    }
  }
}

Query Parameters

quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
molecular_trait_id – molecular phenotype identifier; will return only associations from this molecular phenotype (ENSG00000187583)
variant_id – variant identifier, either rsID (rs577290214) or in the form CHR_BP_REF_ALT (chr7_27916_T_C); will only return associations with this variant
qtl_group – QTL group/context so for any study, you can also specify a qtl_group, which will filter to only return data from this context
gene_id – gene identifier; will return only associations with this gene id (ENSG00000073067)
study – study identifer; will return only associations related to that study (Alasoo_2018)
tissue – tissue ontology identifier; will return only associations from this tissue/cell type (CL_0000235)
start – offset number. default is 0
size – number of items returned. default is 20, max is 1000.
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/associations/(string: rsid)

GET /eqtl/api/associations/(string: variant_id)

Search Variant Associations

Lists all of the associations of the variant requested. Variant id must be a valid rsid. Will return 404 Not Found if the variant id does not exist. If study_accession query parameter is specified, you will get a single association resource in response. Can be specify by p-value cutoff threshold.

Example request:

GET /associations/rs200141179 HTTP/1.1
Host: www.ebi.ac.uk

GET /associations/chr19_230130_GATC_G HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
   "_embedded": {
     "associations": {
       "0": {
         "alt": "G",
         "condition": "naive",
         "rsid": "rs200141179",
         "condition_label": "naive",
         "ac": 240,
         "position": 230130,
         "chromosome": "19",
         "an": 972,
         "qtl_group": "brain",
         "beta": -0.0529243,
         "r2": 0.48226,
         "variant": "chr19_230130_GATC_G",
         "study_id": "BrainSeq",
         "ref": "GATC",
         "tissue_label": "brain",
         "type": "INDEL",
         "maf": 0.246914,
         "median_tpm": 12.272,
         "pvalue": 0.0166984,
         "neg_log10_p_value": 1.77732514,
         "molecular_trait_id": "ENSG00000011304",
         "gene_id": "ENSG00000011304",
         "tissue": "UBERON_0009834",
       },
       "1": {
         "alt": "G",
         "condition": "naive",
         "rsid": "rs200141179",
         "condition_label": "naive",
         "ac": 240,
         "position": 230130,
         "chromosome": "19",
         "an": 972,
         "qtl_group": "brain",
         "beta": 0.0340718,
         "r2": 0.48226,
         "variant": "chr19_230130_GATC_G",
         "study_id": "BrainSeq",
         "ref": "GATC",
         "tissue_label": "brain",
         "type": "INDEL",
         "maf": 0.246914,
         "median_tpm": 27.623,
         "pvalue": 0.424836,
         "neg_log10_p_value": 0.371778689,
         "molecular_trait_id": "ENSG00000129951",
         "gene_id": "ENSG00000129951",
         "tissue": "UBERON_0009834",
       }
     }
   },
   "_links": {
     "self": {
       "href": "http://www.ebi.ac.uk/eqtl/api/associations"
     },
     "first": {
       "href": "http://www.ebi.ac.uk/eqtl/api/associations?start=0&size=2"
     },
     "next": {
       "href": "http://www.ebi.ac.uk/eqtl/api/associations?start=2&size=2"
     }
   }
 }

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20
quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
molecular_trait_id – molecular phenotype identifier; will return only associations from this molecular phenotype (ENSG00000187583)
gene_id – gene identifier; will return only associations with this gene id (ENSG00000073067)
study – study identifer; will return only associations related to that study (Alasoo_2018)
qtl_group – QTL group/context
tissue – tissue ontology identifier; will return only associations from this tissue/cell type (CL_0000235)
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/chromosomes

Chromosomes

Lists all chromosome resources. Note that chromosomes values ‘X’, ‘Y’ and ‘MT’ are mapped to 23, 24 and 25, respectively.

Example request:

GET /chromosomes HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "chromosomes": [
      {
        "chromosome": "1",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1/associations"
          }
        }
      },
      {
        "chromosome": "10",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/10"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/10/associations"
          }
        }
      },
      {
        "chromosome": "11",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/11"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/11/associations"
          }
        }
      },
      {
        "chromosome": "12",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/12"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/12/associations"
          }
        }
      },
      {
        "chromosome": "13",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/13"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/13/associations"
          }
        }
      },
      {
        "chromosome": "14",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/14"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/14/associations"
          }
        }
      },
      {
        "chromosome": "15",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/15"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/15/associations"
          }
        }
      },
      {
        "chromosome": "16",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/16"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/16/associations"
          }
        }
      },
      {
        "chromosome": "17",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/17"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/17/associations"
          }
        }
      },
      {
        "chromosome": "18",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/18"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/18/associations"
          }
        }
      },
      {
        "chromosome": "19",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/19"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/19/associations"
          }
        }
      },
      {
        "chromosome": "2",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/2"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/2/associations"
          }
        }
      },
      {
        "chromosome": "20",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/20"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/20/associations"
          }
        }
      },
      {
        "chromosome": "21",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/21"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/21/associations"
          }
        }
      },
      {
        "chromosome": "22",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/22"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/22/associations"
          }
        }
      }
    ]
  }
}

Status Codes

200 OK – no error

GET /eqtl/api/chromosomes/(string: chromosome)

Chromosome Resource

List a specific chromosome resource. Note that chromosomes values ‘X’, ‘Y’ and ‘MT’ are mapped to 23, 24 and 25, respectively.

Example request:

GET /chromosomes/11 HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/11"
    },
    "associations": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/11/associations"
    }
  },
  "chromosome": "11"
}

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/chromosomes/(string: chromosome)/associations

Search Chromosome Associations

Returns associations for a specific chromosome.

Example request:

GET /chromosomes/1/associations HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "associations": {
      "0": {
        "an": 972,
        "beta": 0.0866221,
        "median_tpm": 0.991,
        "qtl_group": "brain",
        "r2": 0.9107,
        "condition": "naive",
        "variant": "chr1_1053768_G_A",
        "tissue_label": "brain",
        "study_id": "BrainSeq",
        "condition_label": "naive",
        "ref": "G",
        "alt": "A",
        "position": 1053768,
        "pvalue": 0.483624,
        "neg_log10_p_value": 0.315492155,
        "maf": 0.0123457,
        "type": "SNP",
        "ac": 12,
        "rsid": "rs115061121",
        "chromosome": 1,
        "molecular_trait_id": "ENSG00000008128",
        "gene_id": "ENSG00000008128",
        "tissue": "UBERON_0009834",
      },
      "1": {
        "an": 972,
        "beta": 0.0304911,
        "median_tpm": 21.145,
        "qtl_group": "brain",
        "r2": 0.9107,
        "condition": "naive",
        "variant": "chr1_1053768_G_A",
        "tissue_label": "brain",
        "study_id": "BrainSeq",
        "condition_label": "naive",
        "ref": "G",
        "alt": "A",
        "position": 1053768,
        "pvalue": 0.468078,
        "neg_log10_p_value": 0.329681771,
        "maf": 0.0123457,
        "type": "SNP",
        "ac": 12,
        "rsid": "rs115061121",
        "chromosome": 1,
        "molecular_trait_id": "ENSG00000197530",
        "gene_id": "ENSG00000197530",
        "tissue": "UBERON_0009834",
      }
    }
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1/associations"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1/associations?size=2&start=0"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1/associations?size=2&start=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20
quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
bp_lower – lower base pair location threshold, expressed as an integer
bp_upper – upper base pair location threshold, expressed as an integer
molecular_trait_id – molecular phenotype identifier; will return only associations from this molecular phenotype (ENSG00000187583)
gene_id – gene identifier; will return only associations with this gene id (ENSG00000073067)
study – study identifer; will return only associations related to that study (Alasoo_2018)
qtl_group – QTL group/context
tissue – tissue ontology identifier; will return only associations from this tissue/cell type (CL_0000235)
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/chromosomes/(string: chromosome)/associations/(string: variant_id)

Search Variant on Chromosome

Lists all of the associations of the variant requested. Variant id must be a valid rsid. Will return 404 Not Found if the variant id does not exist. Can specify by p-value cutoff threshold. The response should be identical to the /associations/<string:variant_id> but the query time may be faster.

Example request:

GET /chromosomes/1/associations/rs56197012 HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "associations": {
      "0": {
        "study_id": "Nedelec_2016",
        "r2": 0.7364,
        "median_tpm": 148.732,
        "type": "INDEL",
        "condition_label": "naive",
        "chromosome": "1",
        "maf": 0.190184,
        "beta": -0.0255253,
        "condition": "naive",
        "alt": "TAA",
        "ac": 264,
        "an": 326,
        "qtl_group": "macrophage_naive",
        "ref": "T",
        "pvalue": 0.24666,
        "neg_log10_p_value": 0.607901273,
        "position": 814583,
        "variant": "rs56197012",
        "tissue_label": "macrophage",
        "rsid": "rs56197012",
        "molecular_trait_id": "ENSG00000078808",
        "gene_id": "ENSG00000078808",
        "tissue": "CL_0000235",
      },
      "1": {
        "study_id": "Nedelec_2016",
        "r2": 0.7364,
        "median_tpm": 39.017,
        "type": "INDEL",
        "condition_label": "naive",
        "chromosome": "1",
        "maf": 0.190184,
        "beta": 0.018958,
        "condition": "naive",
        "alt": "TAA",
        "ac": 264,
        "an": 326,
        "qtl_group": "macrophage_naive",
        "ref": "T",
        "pvalue": 0.711897,
        "neg_log10_p_value": 0.147582837,
        "position": 814583,
        "variant": "rs56197012",
        "tissue_label": "macrophage",
        "rsid": "rs56197012",
        "molecular_trait_id": "ENSG00000008130",
        "gene_id": "ENSG00000008130",
        "tissue": "CL_0000235",
      }
    }
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1/associations/rs56197012"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1/associations/rs56197012?start=0&size=2"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/chromosomes/1/associations/rs56197012?start=2&size=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20
quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
bp_lower – lower base pair location threshold, expressed as an integer
bp_upper – upper base pair location threshold, expressed as an integer
molecular_trait_id – molecular phenotype identifier; will return only associations from this molecular phenotype (ENSG00000187583)
gene_id – gene identifier; will return only associations with this gene id (ENSG00000073067)
study – study identifer; will return only associations related to that study (Alasoo_2018)
qtl_group – QTL group/context
tissue – tissue ontology identifier; will return only associations from this tissue/cell type (CL_0000235)
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/genes

Genes

Lists all of the existing gene resources.

Example request:

GET /genes HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "gene": [
      {
        "gene": "ENSG00000223972",
        "_links": {
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000223972/associations"
          },
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000223972"
          }
        }
      },
      {
        "gene": "ENSG00000227232",
        "_links": {
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000227232/associations"
          },
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000227232"
          }
        }
      }
    ]
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes?start=0&size=2"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes?start=2&size=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20

Status Codes

200 OK – no error

GET /eqtl/api/genes/(string: gene_id)

Gene Resource

Lists a specific gene resource

Example request:

GET /genes/ENSG00000223972 HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "gene": "ENSG00000223972",
  "_links": {
    "associations": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000223972/associations"
    },
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000223972"
    }
  }
}

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/genes/(string: gene_id)/associations

Search Gene for Associations

Lists associations for a specific gene id.

Example request:

GET /genes/ENSG00000070031/associations HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "associations": {
      "0": {
        "an": 972,
        "beta": -0.116221,
        "median_tpm": 0.561,
        "qtl_group": "brain",
        "r2": 0.5648,
        "study_id": "BrainSeq",
        "condition": "naive",
        "tissue_label": "brain",
        "variant": "chr11_192658_T_C",
        "condition_label": "naive",
        "ref": "T",
        "alt": "C",
        "position": 192658,
        "pvalue": 0.644378,
        "neg_log10_p_value": 0.190859295,
        "maf": 0.00925926,
        "type": "SNP",
        "ac": 9,
        "rsid": "rs373952992",
        "chromosome": "11",
        "molecular_trait_id": "ENSG00000070031",
        "gene_id": "ENSG00000070031",
        "tissue": "UBERON_0009834",
      },
      "1": {
        "an": 972,
        "beta": -0.19745,
        "median_tpm": 0.561,
        "qtl_group": "brain",
        "r2": 0.77945,
        "study_id": "BrainSeq",
        "condition": "naive",
        "tissue_label": "brain",
        "variant": "chr11_193051_G_A",
        "condition_label": "naive",
        "ref": "G",
        "alt": "A",
        "position": 193051,
        "pvalue": 0.166599,
        "neg_log10_p_value": 0.77832761,
        "maf": 0.0277778,
        "type": "SNP",
        "ac": 27,
        "rsid": "rs144999256",
        "chromosome": "11",
        "molecular_trait_id": "ENSG00000070031",
        "gene_id": "ENSG00000070031",
        "tissue": "UBERON_0009834",
       }
     }
   },
   "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000070031/associations"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000070031/associations?start=0&size=2"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/genes/ENSG00000070031/associations?start=1&size=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20
quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
study – study identifer; will return only associations related to that study (Alasoo_2018)
qtl_group – QTL group/context
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)
tissue – tissue ontology identifier; will return only associations from this tissue/cell type (CL_0000235)
variant_id – variant identifier, either rsID (rs577290214) or in the form CHR_BP_REF_ALT (chr7_27916_T_C); will only return associations with this variant
molecular_trait_id – molecular phenotype identifier; will return only associations from this molecular phenotype (ENSG00000187583)

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/molecular_phenotypes

Molecular phenotypes

Lists all of the existing molecular phenotype resources.

Example request:

GET /traits HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "molecular_trait_id": [
      {
        "molecular_trait_id": "ENSG00000187583",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000187583"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000187583/associations"
          }
        }
      },
      {
        "molecular_trait_id": "ENSG00000227232",
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000227232"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000227232/associations"
          }
        }
      }
    ]
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes?start=0&size=2"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes?start=2&size=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20

Status Codes

200 OK – no error

GET /eqtl/api/molecular_phenotypes/(string: molecular_trait_id)

Molecular phenotype Resource

Lists a specific molecular phenotype resource

Example request:

GET /molecular_phenotypes/ENSG00000187583 HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "molecular_trait_id": "ENSG00000187583",
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000187583"
    },
    "associations": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000187583/associations"
    }
  }
}

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/molecular_phenotypes/(string: molecular_trait_id)/associations

Search Molecular phenotype for Associations

Lists associations for a specific molecular trait id.

Example request:

GET /molecular_phenotypes/ENSG00000011304/associations HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
   "_embedded": {
     "associations": {
       "0": {
         "alt": "G",
         "condition": "naive",
         "rsid": "rs200141179",
         "condition_label": "naive",
         "ac": 240,
         "position": 230130,
         "chromosome": "19",
         "an": 972,
         "qtl_group": "brain",
         "beta": -0.0529243,
         "r2": 0.48226,
         "variant": "chr19_230130_GATC_G",
         "study_id": "BrainSeq",
         "ref": "GATC",
         "tissue_label": "brain",
         "type": "INDEL",
         "maf": 0.246914,
         "median_tpm": 12.272,
         "pvalue": 0.0166984,
         "neg_log10_p_value": 1.77732514,
         "molecular_trait_id": "ENSG00000011304",
         "gene_id": "ENSG00000011304",
         "tissue": "UBERON_0009834",
       },
   "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000011304/associations"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000011304/associations?start=0&size=1"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/molecular_phenotypes/ENSG00000011304/associations?start=1&size=1"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20
quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
gene_id – gene identifier; will return only associations with this gene id (ENSG00000073067)
study – study identifer; will return only associations related to that study (Alasoo_2018)
qtl_group – QTL group/context
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)
tissue – tissue ontology identifier; will return only associations from this tissue/cell type (CL_0000235)
variant_id – variant identifier, either rsID (rs577290214) or in the form CHR_BP_REF_ALT (chr7_27916_T_C); will only return associations with this variant

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/qtl_groups

QTL groups

Lists all of the existing qtl groups.

Example request:

GET /qtl_groups HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "qtl_groups": [
      {
        "qtl_group": "Adipose_Subcutaneous"
      },
      {
        "qtl_group": "Adipose_Visceral_Omentum"
      }
    ]
  },
  "_links": {
    "self": {
      "href": "http://localhost:8000/eqtl/api/qtl_groups"
    },
    "first": {
      "href": "http://localhost:8000/eqtl/api/qtl_groups?start=0&size=2"
    },
    "next": {
      "href": "http://localhost:8000/eqtl/api/qtl_groups?start=2&size=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20

Status Codes

200 OK – no error

GET /eqtl/api/studies

Studies

Lists all of the existing study resources.

Example request:

GET /studies HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "studies": [
      [
        {
          "_links": {
            "self": {
              "href": "http://www.ebi.ac.uk/eqtl/api/studies/Alasoo_2018"
            },
            "associations": {
              "href": "http://www.ebi.ac.uk/eqtl/api/studies/Alasoo_2018/associations"
            },
            "tissue": {
              "href": "http://www.ebi.ac.uk/eqtl/api/tissues?study_accession=Alasoo_2018"
            }
          },
          "study_accession": "Alasoo_2018"
        }
      ],
      [
        {
          "_links": {
            "self": {
              "href": "http://www.ebi.ac.uk/eqtl/api/studies/BLUEPRINT"
            },
            "associations": {
              "href": "http://www.ebi.ac.uk/eqtl/api/studies/BLUEPRINT/associations"
            },
            "tissue": {
              "href": "http://www.ebi.ac.uk/eqtl/api/tissues?study_accession=BLUEPRINT"
            }
          },
          "study_accession": "BLUEPRINT"
        }
      ]
    ]
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/studies"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/studies?start=0&size=2"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/studies?start=2&size=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20

Status Codes

200 OK – no error

GET /eqtl/api/tissues

Tissues

Lists all of the existing tissue resources.

Example request:

GET /tissues HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
   _embedded: {
      tissues: [{
            tissue_label: "Esophagus - Mucosa",
            tissue: "UBER_0006920"
         },
         {
            tissue_label: "Artery - Coronary",
            tissue: "UBER_0001621"
         }
      ]
   },
   _links: {
      self: {
         href: "http://www.ebi.ac.uk/eqtl/api/tissues"
      },
      first: {
         href: "http://www.ebi.ac.uk/eqtl/api/tissues?start=0&size=2"
      },
      next: {
         href: "http://www.ebi.ac.uk/eqtl/api/tissues?start=2&size=2"
      }
   }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20

Status Codes

200 OK – no error

GET /eqtl/api/tissues/(string: tissue)

Tissue

Example request:

GET /tissues/CL_0000057 HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_links": {
    "associations": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000057/associations"
    },
    "studies": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000057/studies"
    },
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000057"
    }
  },
  "tissue": "CL_0000057"
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/tissues/(string: tissue)/associations

Search Tissue for Associations

Lists associations for a specific tissue ontology

Example request:

GET /tissues/CL_0000235/associations HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "associations": {
      "0": {
        "condition_label": "IFNg_18h+Salmonella_5h",
        "alt": "A",
        "condition": "IFNg+Salmonella",
        "rsid": "rs201551942",
        "r2": 0.44038,
        "ac": 64,
        "position": 229783,
        "chromosome": "19",
        "an": 168,
        "qtl_group": "macrophage_IFNg+Salmonella",
        "beta": 0.0245131,
        "median_tpm": null,
        "variant": "chr19_229783_G_A",
        "study_id": "Alasoo_2018",
        "ref": "G",
        "tissue_label": "macrophage",
        "type": "SNP",
        "maf": 0.380952,
        "pvalue": 0.5004,
        "neg_log10_p_value": 0.300682699,
        "molecular_trait_id": "ENSG00000011304",
        "gene_id": "ENSG00000011304",
        "tissue": "CL_0000235",
      },
      "1": {
        "condition_label": "IFNg_18h+Salmonella_5h",
        "alt": "A",
        "condition": "IFNg+Salmonella",
        "rsid": "rs201551942",
        "r2": 0.44038,
        "ac": 64,
        "position": 229783,
        "chromosome": "19",
        "an": 168,
        "qtl_group": "macrophage_IFNg+Salmonella",
        "beta": -0.0685795,
        "median_tpm": null,
        "variant": "chr19_229783_G_A",
        "study_id": "Alasoo_2018",
        "ref": "G",
        "tissue_label": "macrophage",
        "type": "SNP",
        "maf": 0.380952,
        "pvalue": 0.0528997,
        "neg_log10_p_value": 1.276546791,
        "molecular_trait_id": "ENSG00000099817",
        "gene_id": "ENSG00000099817",
        "tissue": "CL_0000235",
      }
    }
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/associations"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/associations?size=2&start=0"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/associations?size=2&start=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20
quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
gene_id – gene identifier; will return only associations with this gene id (ENSG00000073067)
study – study identifer; will return only associations related to that study (Alasoo_2018)
qtl_group – QTL group/context
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)
molecular_trait_id – molecular phenotype identifier; will return only associations from this molecular phenotype (ENSG00000187583)
variant_id – variant identifier, either rsID (rs577290214) or in the form CHR_BP_REF_ALT (chr7_27916_T_C); will only return associations with this variant

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/tissues/(string: tissue)/studies

Studies for tissues

Lists all of the existing study resources.

Example request:

GET /tissues/CL_0000235/studies HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "studies": [
      {
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies/Alasoo_2018"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies/Alasoo_2018/associations"
          },
          "tissue": {
            "href": "http://www.ebi.ac.uk/eqtl/api/tissues?study_accession=Alasoo_2018"
          }
        },
        "study_accession": "Alasoo_2018"
      },
      {
        "_links": {
          "self": {
            "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies/Nedelec_2016"
          },
          "associations": {
            "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies/Nedelec_2016/associations"
          },
          "tissue": {
            "href": "http://www.ebi.ac.uk/eqtl/api/tissues?study_accession=Nedelec_2016"
          }
        },
        "study_accession": "Nedelec_2016"
      }
    ]
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies?size=20&start=0"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20

Status Codes

200 OK – no error

GET /eqtl/api/tissues/(string: tissue)/studies/(string: study)

GET /eqtl/api/studies/(string: study)

Study

Example request:

GET /studies/Alasoo_2018 HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "study_accession": "Alasoo_2018",
  "_links": {
    "associations": {
      "href": "http://www.ebi.ac.uk/eqtl/api/studies/Alasoo_2018/associations"
    },
    "tissue": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues?study_accession=Alasoo_2018"
    },
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/studies/Alasoo_2018"
    }
  }
}

Status Codes

200 OK – no error
404 Not Found – not found error

GET /eqtl/api/tissues/(string: tissue)/studies/(string: study)/associations

GET /eqtl/api/studies/(study)/associations

Search Study for Associations

Lists associations for a specific study.

Example request:

GET /studies/Alasoo_2018/associations HTTP/1.1
Host: www.ebi.ac.uk

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

{
  "_embedded": {
    "associations": {
      "0": {
        "study_id": "Alasoo_2018",
        "r2": 0.44038,
        "median_tpm": null,
        "type": "SNP",
        "condition_label": "IFNg_18h+Salmonella_5h",
        "chromosome": "19",
        "maf": 0.380952,
        "beta": 0.0245131,
        "condition": "IFNg+Salmonella",
        "alt": "A",
        "ac": 64,
        "an": 168,
        "qtl_group": "macrophage_IFNg+Salmonella",
        "ref": "G",
        "pvalue": 0.5004,
        "neg_log10_p_value": 0.300682699,
        "position": 229783,
        "variant": "chr19_229783_G_A",
        "tissue_label": "macrophage",
        "rsid": "rs201551942",
        "molecular_trait_id": "ENSG00000011304",
        "gene_id": "ENSG00000011304",
        "tissue": "CL_0000235",
      },
      "1": {
        "study_id": "Alasoo_2018",
        "r2": 0.44038,
        "median_tpm": null,
        "type": "SNP",
        "condition_label": "IFNg_18h+Salmonella_5h",
        "chromosome": "19",
        "maf": 0.380952,
        "beta": -0.0685795,
        "condition": "IFNg+Salmonella",
        "alt": "A",
        "ac": 64,
        "an": 168,
        "qtl_group": "macrophage_IFNg+Salmonella",
        "ref": "G",
        "pvalue": 0.0528997,
        "neg_log10_p_value": 1.276546791,
        "position": 229783,
        "variant": "chr19_229783_G_A",
        "tissue_label": "macrophage",
        "rsid": "rs201551942",
        "molecular_trait_id": "ENSG00000099817",
        "gene_id": "ENSG00000099817",
        "tissue": "CL_0000235",
      }
    }
  },
  "_links": {
    "self": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies/Alasoo_2018/associations"
    },
    "first": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies/Alasoo_2018/associations?start=0&size=2"
    },
    "next": {
      "href": "http://www.ebi.ac.uk/eqtl/api/tissues/CL_0000235/studies/Alasoo_2018/associations?start=2&size=2"
    }
  }
}

Query Parameters

start – offset number. default is 0
size – number of items returned. default is 20
quant_method – ge (default), exon, microarray, tx or txrev will show you the association data for different quantification methods. See the API documentation for more details.
p_lower – lower p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
p_upper – upper p-value threshold, can be expressed as a float or using mantissa and exponent annotation (0.001 or 1e-3 or 1E-3)
gene_id – gene identifier; will return only associations with this gene id (ENSG00000073067)
molecular_trait_id – molecular phenotype identifier; will return only associations from this molecular phenotype (ENSG00000187583)
qtl_group – QTL group/context
paginate – Flag whether the response should be paginated or not. Boolean True (default) or False
links – Flag whether the response should contain association level links or not. Boolean True or False (default)
tissue – tissue ontology identifier; will return only associations from this tissue/cell type (CL_0000235)
variant_id – variant identifier, either rsID (rs577290214) or in the form CHR_BP_REF_ALT (chr7_27916_T_C); will only return associations with this variant

Status Codes

200 OK – no error
404 Not Found – not found error