Genes Variants

curl --request GET \
  --url https://catalog-api-dev.demo.igvf.org/api/genes/variants

import requests

url = "https://catalog-api-dev.demo.igvf.org/api/genes/variants"

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

fetch('https://catalog-api-dev.demo.igvf.org/api/genes/variants', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

[
  {
    "gene": "<string>",
    "sequence_variant": "<string>",
    "source": "<string>",
    "source_url": "<string>",
    "label": "<string>",
    "biological_context": "<string>",
    "biosample_term": "<string>",
    "intron_chr": "<string>",
    "intron_start": "<string>",
    "intron_end": "<string>",
    "effect_size": 123,
    "neg_log10_pvalue": 123,
    "neg_log10_pvalue_adj": 123,
    "log2FC": 123,
    "posterior_inclusion_probability": 123,
    "coefficient_stddev": 123,
    "power": 123,
    "significant": true,
    "standard_error": 123,
    "z_score": 123,
    "credible_set_min_r2": 123,
    "method": "<string>",
    "crispr_modality": "<string>",
    "p_value": 123,
    "chr": "<string>",
    "study": "<string>",
    "name": "<string>",
    "class": "<string>"
  }
]

{
  "message": "<string>",
  "code": "<string>",
  "issues": [
    {
      "message": "<string>"
    }
  ]
}

API Reference

Genes Variants

Retrieve variant-gene pairs including eQTLs & splice QTLs from AFGR and eQTL Catalogue, and CRISPR screen and Variant-EFFECTS from IGVF, by Ensembl gene ids.

The following parameters can be used to set thresholds on -log10 p_value: gt (>), gte (>=), lt (<), lte (<=).

Set verbose = true to retrieve full info on the corresponding variants and genes.

At least one of these properties must be defined: gene_id, hgnc_id, gene_name, region, alias, method, or files_fileset.

The limit parameter controls the page size and can not exceed 500.

Pagination is 0-based.

Examples by method

These examples are grouped by method; use the method filter to return data from a specific method.

eQTL:

Single result

gene_id = ENSG00000187642
neg_log10_pvalue = gte:24.5
method = eQTL

Group results

alias = PERM1
method = eQTL

spliceQTL:

Single result

gene_id = ENSG00000188976
neg_log10_pvalue = gt:45
effect_size = gt:0.5
method = spliceQTL

Group results

alias = NOC2L
method = spliceQTL

Variant-EFFECTS:

Single result

gene_id = ENSG00000108179
neg_log10_pvalue = gt:13.1
method = Variant-EFFECTS

Group results

alias = PPIF
method = Variant-EFFECTS

CRISPR screen:

query by gene identifier

gene_id = ENSG00000177455
method = CRISPR screen

query by gene name

gene_name = CD19
method = CRISPR screen

Genes Variants

curl --request GET \
  --url https://catalog-api-dev.demo.igvf.org/api/genes/variants

import requests

url = "https://catalog-api-dev.demo.igvf.org/api/genes/variants"

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

fetch('https://catalog-api-dev.demo.igvf.org/api/genes/variants', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

[
  {
    "gene": "<string>",
    "sequence_variant": "<string>",
    "source": "<string>",
    "source_url": "<string>",
    "label": "<string>",
    "biological_context": "<string>",
    "biosample_term": "<string>",
    "intron_chr": "<string>",
    "intron_start": "<string>",
    "intron_end": "<string>",
    "effect_size": 123,
    "neg_log10_pvalue": 123,
    "neg_log10_pvalue_adj": 123,
    "log2FC": 123,
    "posterior_inclusion_probability": 123,
    "coefficient_stddev": 123,
    "power": 123,
    "significant": true,
    "standard_error": 123,
    "z_score": 123,
    "credible_set_min_r2": 123,
    "method": "<string>",
    "crispr_modality": "<string>",
    "p_value": 123,
    "chr": "<string>",
    "study": "<string>",
    "name": "<string>",
    "class": "<string>"
  }
]

{
  "message": "<string>",
  "code": "<string>",
  "issues": [
    {
      "message": "<string>"
    }
  ]
}

Query Parameters

gene_id

string

hgnc_id

string

gene_name

string

alias

string

neg_log10_pvalue

string

effect_size

string

biosample_term

string

biological_context

string

label

enum<string>

Available options:

eQTL,

spliceQTL,

variant effect on gene expression

method

enum<string>

Available options:

CRISPR screen,

Variant-EFFECTS,

eQTL,

spliceQTL

files_fileset

string

source

enum<string>

Available options:

AFGR,

EBI,

IGVF

name

enum<string>

Available options:

expression modulated by,

splicing modulated by

organism

enum<string>

default:Homo sapiens

Available options:

Homo sapiens

verbose

enum<string>

default:false

Available options:

true,

false

page

number

default:0

limit

number

Response

Successful response

gene

required

sequence_variant

required

source

string

required

source_url

string

required

label

string

required

biological_context

string

required

biosample_term

string

required

intron_chr

string | null

intron_start

string | null

intron_end

string | null

effect_size

number | null

neg_log10_pvalue

neg_log10_pvalue_adj

number | null

log2FC

number | null

posterior_inclusion_probability

number | null

coefficient_stddev

number | null

power

number | null

significant

boolean | null

standard_error

number | null

z_score

number | null

credible_set_min_r2

number | null

method

string | null

crispr_modality

string | null

p_value

number | null

chr

string | null

study

name

string | null

class

string | null

Genes Proteins Genes Diseases

Overview

Endpoints

Genes Variants

Query Parameters

Response