Regions
On this page, we’ll dive into the /v1/regions/ endpoint. This endpoint allows you to query for regions and their variants. The response is a list of variants, and pagination is supported.
Retrieve a region
This endpoint allows you to retrieve a region by specifying region in chr-startPosition-endPosition format. The response is a list of variants, and pagination is supported. Refer to the region model for more information on the properties returned.
Path parameters
- Name
region- Type
- string
- Description
The region to retrieve. The region should be specified in chr-startPosition-endPosition format.
Query parameters
- Name
page- Type
- integer
- Description
The page number to browse.
- Name
limit- Type
- integer
- Description
The number of objects to return per page.
Attributes
- Name
data- Type
- list
- Description
The list of objects returned by the query.
- Name
has_more- Type
- bool
- Description
Indicates whether there are more pages to browse.
- Name
count- Type
- integer
- Description
The total number of objects that match the query.
Request
curl -G https://api.genohub.org/v1/regions/19-44851820-44908922
Paginated response
{
"count": 16400,
"has_more": true,
"data": [
{
"variant_vcf": "19-44908922-G-A",
"chromosome": "19",
"position": "44908922",
"genecode_comprehensive_info": "APOE",
"bravo_an": "264690",
"bravo_ac": "2",
"bravo_af": "0.00000755601",
"filter_status": "PASS",
"genecode_comprehensive_category": "exonic",
"genecode_comprehensive_exonic_category": "nonsynonymous SNV",
"metasvm_pred": "T",
// ...
},
{
"variant_vcf": "19-44908921-C-T",
"chromosome": "19",
"position": "44908921",
"genecode_comprehensive_info": "APOE",
"bravo_an": "264690",
"bravo_ac": "6",
"bravo_af": "0.000022668",
"filter_status": "PASS",
"genecode_comprehensive_category": "exonic",
"genecode_comprehensive_exonic_category": "nonsynonymous SNV",
"metasvm_pred": "T",
// ...
},
// ...
]}
Retrieve a region's SNV variants
This endpoint allows you to retrieve a region SNV variants by specifying region in chr-startPosition-endPosition format. The response is a list of SNV variants, and pagination is supported. Refer to the region model for more information on the properties returned.
Path parameters
- Name
region- Type
- string
- Description
The region to retrieve. The region should be specified in chr-startPosition-endPosition format.
Query parameters
- Name
page- Type
- integer
- Description
The page number to browse.
- Name
limit- Type
- integer
- Description
The number of objects to return per page.
Attributes
- Name
data- Type
- list
- Description
The list of objects returned by the query.
- Name
has_more- Type
- bool
- Description
Indicates whether there are more pages to browse.
- Name
count- Type
- integer
- Description
The total number of objects that match the query.
Request
curl -G https://api.genohub.org/v1/regions/19-44851820-44908922/snv
Paginated response
{
"count": 15104,
"has_more": true,
"data": [
{
"variant_vcf": "19-44908922-G-A",
"chromosome": "19",
"position": "44908922",
"genecode_comprehensive_info": "APOE",
"bravo_an": "264690",
"bravo_ac": "2",
"bravo_af": "0.00000755601",
"filter_status": "PASS",
"genecode_comprehensive_category": "exonic",
"genecode_comprehensive_exonic_category": "nonsynonymous SNV",
"metasvm_pred": "T",
// ...
},
{
"variant_vcf": "19-44908921-C-T",
"chromosome": "19",
"position": "44908921",
"genecode_comprehensive_info": "APOE",
"bravo_an": "264690",
"bravo_ac": "6",
"bravo_af": "0.000022668",
"filter_status": "PASS",
"genecode_comprehensive_category": "exonic",
"genecode_comprehensive_exonic_category": "nonsynonymous SNV",
"metasvm_pred": "T",
// ...
},
// ...
]}
Retrieve a region's InDEL variants
This endpoint allows you to retrieve a region InDEL variants by specifying region in chr-startPosition-endPosition format. The response is a list of InDEL variants, and pagination is supported. Refer to the region model for more information on the properties returned.
Path parameters
- Name
region- Type
- string
- Description
The region to retrieve. The region should be specified in chr-startPosition-endPosition format.
Query parameters
- Name
page- Type
- integer
- Description
The page number to browse.
- Name
limit- Type
- integer
- Description
The number of objects to return per page.
Attributes
- Name
data- Type
- list
- Description
The list of objects returned by the query.
- Name
has_more- Type
- bool
- Description
Indicates whether there are more pages to browse.
- Name
count- Type
- integer
- Description
The total number of objects that match the query.
Request
curl -G https://api.genohub.org/v1/regions/19-44851820-44908922/indel
Paginated response
{
"count": 1296,
"has_more": true,
"data": [
{
"variant_vcf": "19-44908859-C-CCGAGCGCGGCCTCAGCGCCATCCG",
"chromosome": "19",
"position": "44908859",
"genecode_comprehensive_info": "APOE",
"bravo_an": "264690",
"bravo_ac": "1",
"bravo_af": "0.000003778",
"filter_status": "PASS",
"genecode_comprehensive_category": "exonic",
"genecode_comprehensive_exonic_category": "nonframeshift insertion",
"metasvm_pred": "",
// ...
},
{
"variant_vcf": "19-44908840-GC-G",
"chromosome": "19",
"position": "44908840",
"genecode_comprehensive_info": "APOE",
"bravo_an": "264690",
"bravo_ac": "1",
"bravo_af": "0.000003778",
"filter_status": "PASS",
"genecode_comprehensive_category": "exonic",
"genecode_comprehensive_exonic_category": "frameshift deletion",
"metasvm_pred": "",
// ...
},
// ...
]}
The region model
The region model is similar to the gene model, and a subset of the variant model. The region model contains the following properties:
Properties
- Name
variant_vcf- Type
- string
- Description
The unique identifier of the given variant. Reported as chr-pos-ref-alt format.
- Name
chromosome- Type
- string
- Description
The chromosome where the variant is located
- Name
position- Type
- string
- Description
The position of the variant
- Name
genecode_comprehensive_info- Type
- string
- Description
Identify whether variants cause protein coding changes using Gencode genes definition systems, it will label the gene name of the variants has impact, if it is intergenic region, the nearby gene name will be labeled in the annotation. (Frankish et al., 2018; Harrow et al., 2012)
- Name
bravo_an- Type
- string
- Description
TOPMed Bravo Genome Allele Number. (NHLBI TOPMed Consortium, 2018; Taliun et al., 2019)
- Name
bravo_ac- Type
- string
- Description
TOPMed Bravo Genome Allele Count.
- Name
bravo_af- Type
- string
- Description
TOPMed Bravo Genome Allele Frequency. (NHLBI TOPMed Consortium, 2018; Taliun et al., 2019)
- Name
filter_status- Type
- string
- Description
TOPMed QC status of the given variant.
- Name
genecode_comprehensive_category- Type
- string
- Description
Comprehensive category from Genecode
- Name
genecode_comprehensive_exonic_category- Type
- string
- Description
Identify whether variants cause protein coding changes using Gencode genes definition systems. It will label the gene name of the variants has impact, if it is intergenic region, the nearby gene name will be labeled in the annotation.
- Name
metasvm_pred- Type
- string
- Description
Description for MetasvmPred
- Name
rsid- Type
- string
- Description
The rsID of the given variant (if exists).
- Name
cage_enhancer- Type
- string
- Description
CAGE defined permissive Enhancer sites from Fantom 5.
- Name
cage_promoter- Type
- string
- Description
CAGE defined promoter sites from Fantom 5.
- Name
sift_cat- Type
- string
- Description
SIFT category of change.
- Name
polyphen_cat- Type
- string
- Description
PolyPhen category of change.
- Name
cadd_phred- Type
- string
- Description
The CADD score in PHRED scale (integrative score). A higher CADD score indicates more deleterious. Range: [0, 99].
- Name
genehancer- Type
- string
- Description
Predicted human enhancer sites from the GeneHancer database.
- Name
clnsig- Type
- string
- Description
Clinical significance for this single variant. (Landrum et al., 2017, 2013)
- Name
clnsigincl- Type
- string
- Description
Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance. (Landrum et al., 2017, 2013)
- Name
clndn- Type
- string
- Description
Clinical disease name
- Name
clndnincl- Type
- string
- Description
Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance.
- Name
clnrevstat- Type
- string
- Description
ClinVar review status for the Variation ID.
- Name
origin- Type
- string
- Description
Allele origin. One or more of the following values may be added: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512
- tested-inconclusive.
- Name
clndisdb- Type
- string
- Description
Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN.
- Name
clndisdbincl- Type
- string
- Description
For included variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN.
- Name
geneinfo- Type
- string
- Description
Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|).
- Name
linsight- Type
- string
- Description
The LINSIGHT score (integrative score). A higher LINSIGHT score indicates more functionality. Range: [0.215, 0.995].
- Name
fathmm_xf- Type
- string
- Description
The FATHMM-XF score (integrative score). A higher FATHMM-XF score indicates more functionality. Range: [0.405, 99.451].
- Name
apc_conservation_v2- Type
- null.Float
- Description
Conservation annotation PC: the first PC of the standardized scores of “GerpN, GerpS, priPhCons, mamPhCons, verPhCons, priPhyloP, mamPhyloP, verPhyloP” in PHRED scale. Range: [0, 75.824].
- Name
apc_epigenetics_active- Type
- null.Float
- Description
Active Epigenetic annotation PC: the first PC of the standardized scores of “EncodeH3K4me1.max, EncodeH3K4me2.max, EncodeH3K4me3.max, EncodeH3K9ac.max, EncodeH3K27ac.max, EncodeH4K20me1.max，EncodeH2AFZ.max,” in PHRED scale.Range: [0, 86.238].
- Name
apc_epigenetics_repressed- Type
- null.Float
- Description
Repressed Epigenetic annotation PC: the first PC of the standardized scores of “EncodeH3K9me3.max, EncodeH3K27me3.max” in PHRED scale. Range: [0, 86.238].
- Name
apc_epigenetics_transcription- Type
- null.Float
- Description
Transcription Epigenetic annotation PC: the first PC of the standardized scores of “EncodeH3K36me3.max, EncodeH3K79me2.max” in PHRED scale. Range: [0, 86.238].
- Name
apc_local_nucleotide_diversity_v3- Type
- null.Float
- Description
Local nucleotide diversity annotation PC: the first PC of the standardized scores of “bStatistic, RecombinationRate, NuclearDiversity” in PHRED scale. Range: [0, 86.238].
- Name
apc_mappability- Type
- null.Float
- Description
Mappability annotation PC: the first PC of the standardized scores of “umap_k100, bismap_k100, umap_k50, bismap_k50, umap_k36, bismap_k36, umap_k24, bismap_k24” in PHRED scale. Range: [0.007, 22.966].
- Name
apc_mutation_density- Type
- null.Float
- Description
Mutation density annotation PC: the first PC of the standardized scores of “Common100bp, Rare100bp, Sngl100bp, Common1000bp, Rare1000bp, Sngl1000bp, Common10000bp, Rare10000bp, Sngl10000bp” in PHRED scale. Range: [0, 84.477].
- Name
apc_protein_function_v3- Type
- null.Float
- Description
Protein function annotation PC: the first PC of the standardized scores of “SIFTval, PolyPhenVal, Grantham, Polyphen2_HDIV_score, Polyphen2_HVAR_score, MutationTaster_score, MutationAssessor_score” in PHRED scale. Range: [2.974, 86.238].
- Name
apc_transcription_factor- Type
- null.Float
- Description
Transcription factor annotation PC: the first PC of the standardized scores of “RemapOverlapTF, RemapOverlapCL” in PHRED scale. Range: [1.185, 86.238].
- Name
af_total- Type
- string
- Description
GNOMAD v3 Genome Allele Frequency using all the samples.
- Name
tg_afr- Type
- string
- Description
1000 Genomes African population frequency.
- Name
tg_all- Type
- string
- Description
GNOMAD v3 Genome African population frequency. (GNOMAD Consortium, 2019; Karczewski et al., 2020)
- Name
tg_amr- Type
- string
- Description
1000 Genomes Ad Mixed American population frequency.
- Name
tg_eas- Type
- string
- Description
1000 Genomes East Asian population frequency.
- Name
tg_eur- Type
- string
- Description
1000 Genomes European population frequency.
- Name
tg_sas- Type
- string
- Description
1000 Genomes South Asian population frequency.