Variants Phenotypes

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

import requests

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

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

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

[
  {
    "phenotype_id": "<string>",
    "phenotype_term": "<string>",
    "p_value": 123,
    "beta": 123,
    "beta_ci_lower": 123,
    "beta_ci_upper": 123,
    "oddsr_ci_lower": 123,
    "oddsr_ci_upper": 123,
    "lead_chrom": "<string>",
    "lead_pos": 123,
    "lead_ref": "<string>",
    "lead_alt": "<string>",
    "direction": "<string>",
    "name": "<string>",
    "variant": "<string>",
    "rsid": [
      "<string>"
    ],
    "study": "<string>",
    "neg_log10_pvalue": 123,
    "source": "OpenTargets",
    "source_url": "<string>",
    "class": "<string>",
    "method": "<string>",
    "label": "<string>",
    "version": "October 2022 (22.10)"
  }
]

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

API Reference

Variants Phenotypes

Retrieve variant-trait pairs from GWAS, SGE, and cV2F by variants.

Filters on phenotype ontology id can be used together.

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 studies.

At least one of these fields is required: variant_id, spdi, hgvs, rsid, ca_id, region, method, or files_fileset.

The limit parameter controls the page size and can not exceed 100.

Pagination is 0-based.

Examples by method

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

GWAS:

query by variant identifier

spdi = NC_000001.11:5277210:G:A
neg_log10_pvalue = gte:5
method = GWAS

query by region

region = chr1:5270008-5277214
method = GWAS

SGE:

query by variant identifier

spdi = NC_000007.14:152660654:T:A
method = SGE

query by region

region = chr7:152655654-152664654
method = SGE

cV2F:

query by variant identifier

spdi = NC_000001.11:91420:T:C
method = cV2F

query by region

region = chr1:91418-91424
method = cV2F

Variants Phenotypes

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

import requests

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

response = requests.get(url)

print(response.text)

const options = {method: 'GET'};

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

[
  {
    "phenotype_id": "<string>",
    "phenotype_term": "<string>",
    "p_value": 123,
    "beta": 123,
    "beta_ci_lower": 123,
    "beta_ci_upper": 123,
    "oddsr_ci_lower": 123,
    "oddsr_ci_upper": 123,
    "lead_chrom": "<string>",
    "lead_pos": 123,
    "lead_ref": "<string>",
    "lead_alt": "<string>",
    "direction": "<string>",
    "name": "<string>",
    "variant": "<string>",
    "rsid": [
      "<string>"
    ],
    "study": "<string>",
    "neg_log10_pvalue": 123,
    "source": "OpenTargets",
    "source_url": "<string>",
    "class": "<string>",
    "method": "<string>",
    "label": "<string>",
    "version": "October 2022 (22.10)"
  }
]

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

Query Parameters

spdi

string

hgvs

string

rsid

string

ca_id

string

variant_id

string

region

string

phenotype_id

string

neg_log10_pvalue

string

method

enum<string>

Available options:

GWAS,

SGE,

cV2F

label

enum<string>

Available options:

GWAS,

predicted variant effect on phenotype,

protein variant effect

class

enum<string>

Available options:

observed data,

prediction

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

files_fileset

string

Response

Successful response

Option 1
Option 2

phenotype_id

string | null

required

phenotype_term

string | null

required

p_value

number | null

required

beta

number | null

required

beta_ci_lower

number | null

required

beta_ci_upper

number | null

required

oddsr_ci_lower

number | null

required

oddsr_ci_upper

number | null

required

lead_chrom

string | null

required

lead_pos

number | null

required

lead_ref

string | null

required

lead_alt

string | null

required

direction

string | null

required

name

string

required

variant

required

rsid

string[] | null

study

neg_log10_pvalue

number | null

source

string

default:OpenTargets

source_url

string | null

class

string | null

method

string | null

label

string | null

version

string

default:October 2022 (22.10)

Variants Variant Linkage Disequilibrium Variants Biosamples

Overview

Endpoints

Variants Phenotypes

Query Parameters

Response