curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/variants/genomic-elements/genesimport requests
url = "https://catalog-api-dev.demo.igvf.org/api/variants/genomic-elements/genes"
response = requests.get(url)
print(response.text)const options = {method: 'GET'};
fetch('https://catalog-api-dev.demo.igvf.org/api/variants/genomic-elements/genes', options)
.then(res => res.json())
.then(res => console.log(res))
.catch(err => console.error(err));[
{
"variant": {
"chr": "<string>",
"pos": 123,
"ref": "<string>",
"alt": "<string>",
"rsid": [
"<string>"
],
"spdi": "<string>",
"hgvs": "<string>",
"ca_id": "<string>",
"_id": "<string>"
},
"genomic_element": {
"_id": "<string>",
"name": "<string>",
"chr": "<string>",
"start": 123,
"end": 123,
"type": "<string>",
"source": "<string>",
"source_url": "<string>"
},
"gene": {
"_id": "<string>",
"name": "<string>",
"chr": "<string>",
"start": 123,
"end": 123,
"strand": "<string>"
},
"name": "<string>",
"label": "<string>",
"method": "<string>",
"class": "<string>",
"source": "<string>",
"source_url": "<string>",
"files_filesets": "<string>",
"biological_context": "<string>",
"biosample_term": "<string>",
"distance_to_tss": 123,
"crispr_modality": "<string>",
"log2FC": 123,
"neg_log10_pvalue": 123,
"neg_log10_pvalue_adj": 123,
"p_value": 123,
"p_value_adj": 123,
"effect_size": 123,
"significant": true
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}Variants Genomic Elements Genes
Retrieve genes whose expression is modulated by perturbing genomic elements that overlap a variant.
The query starts from a variant, finds overlapping Perturb-seq genomic elements, then returns element-gene associations.
By default (nearby_genes = true), only nearby genes on the same chromosome as the variant are returned, and the overlapping genomic element must be within 2 Mb of the gene TSS; distance_to_tss is included in the response.
Set nearby_genes = false to return all genes linked to the overlapping elements regardless of chromosome or distance.
At least one variant identifier is required: variant_id, spdi, hgvs, or ca_id.
Example: variant_id = NC_000001.11:109426297:G:C,
spdi = NC_000001.11:109426297:G:C,
nearby_genes = true,
files_fileset = IGVFFI0206LUDV,
biological_context = HCASMC-hTERT,
biosample_term = EFO_0022614.
The limit parameter controls the page size and can not exceed 100.
Pagination is 0-based.
curl --request GET \
--url https://catalog-api-dev.demo.igvf.org/api/variants/genomic-elements/genesimport requests
url = "https://catalog-api-dev.demo.igvf.org/api/variants/genomic-elements/genes"
response = requests.get(url)
print(response.text)const options = {method: 'GET'};
fetch('https://catalog-api-dev.demo.igvf.org/api/variants/genomic-elements/genes', options)
.then(res => res.json())
.then(res => console.log(res))
.catch(err => console.error(err));[
{
"variant": {
"chr": "<string>",
"pos": 123,
"ref": "<string>",
"alt": "<string>",
"rsid": [
"<string>"
],
"spdi": "<string>",
"hgvs": "<string>",
"ca_id": "<string>",
"_id": "<string>"
},
"genomic_element": {
"_id": "<string>",
"name": "<string>",
"chr": "<string>",
"start": 123,
"end": 123,
"type": "<string>",
"source": "<string>",
"source_url": "<string>"
},
"gene": {
"_id": "<string>",
"name": "<string>",
"chr": "<string>",
"start": 123,
"end": 123,
"strand": "<string>"
},
"name": "<string>",
"label": "<string>",
"method": "<string>",
"class": "<string>",
"source": "<string>",
"source_url": "<string>",
"files_filesets": "<string>",
"biological_context": "<string>",
"biosample_term": "<string>",
"distance_to_tss": 123,
"crispr_modality": "<string>",
"log2FC": 123,
"neg_log10_pvalue": 123,
"neg_log10_pvalue_adj": 123,
"p_value": 123,
"p_value_adj": 123,
"effect_size": 123,
"significant": true
}
]{
"message": "<string>",
"code": "<string>",
"issues": [
{
"message": "<string>"
}
]
}Query Parameters
true, false Homo sapiens Response
Successful response
Show child attributes
Show child attributes
Show child attributes
Show child attributes
Show child attributes
Show child attributes