Variants Genes

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

import requests

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

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

fetch('https://catalog-api-dev.demo.igvf.org/api/variants/genes', 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

Variants Genes

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

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: spdi, hgvs, rsid, ca_id, variant_id, region, method, or files_filesets.

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

spdi = NC_000001.11:40241653:TGAA:TGAAATTGAA
effect_size = gte:0.3
method = eQTL

Group results

region = chr1:40241650-40241759 (maximum length: 10kb)
method = eQTL

spliceQTL:

Single result

spdi = NC_000001.11:898757:AAAAAA:AAAAAAA
effect_size = gte:0.3
method = spliceQTL

Group results

region = chr1:898750-898759 (maximum length: 10kb)
method = spliceQTL

Variant-EFFECTS:

Single result

spdi = NC_000010.11:79347741:AGGT:TCAG
effect_size = lt:-0.6
method = Variant-EFFECTS

Group results

region = chr10:79347740-79347749 (maximum length: 10kb)
method = Variant-EFFECTS

CRISPR screen:

query by variant identifier

spdi = NC_000016.10:28930710:G:A
method = CRISPR screen

query by region

region = chr16:28930700-28930800 (maximum length: 10kb)
method = CRISPR screen

Variants Genes

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

import requests

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

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

fetch('https://catalog-api-dev.demo.igvf.org/api/variants/genes', 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

spdi

string

hgvs

string

rsid

string

ca_id

string

variant_id

string

region

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:

modulates expression of,

modulates splicing of

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

Variants Frequency Variants Drugs

Overview

Endpoints

Variants Genes

Query Parameters

Response