Computes and returns LD values between the given variant and all other variants in a window centered around the given variant. The window size is set to 500 kb.
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
id | String | Variant id | - |
rs116035550 |
population_name | String | Population for which to compute LD. Use GET /info/variation/populations/:species?filter=LD to retrieve a list of all populations with LD data. | - |
1000GENOMES:phase_3:KHV |
species | String | Species name/alias | - |
homo_sapiens human |
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
attribs | Boolean | Add variation attributes for the variation which is used to compute LD data with the input variation: chr, start, end, strand, consequence_type, clinical_significance | 0 | - |
callback | String | Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. | - |
randomlygeneratedname |
d_prime | Float | Measure of LD. If D' is provided only return pairs of variants whose D' value is equal to or greater than the value provided. | 0 |
1.0 |
r2 | Float | Measure of LD. If r-squared is provided only return pairs of variants whose r-squared value is equal to or greater than the value provided. | 0 |
0.85 |
window_size | Integer | Window size in kb. The maximum allowed value for the window size is 500 kb. LD is computed for the given variant and all variants that are located within the specified window. | 500 |
500 |
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://grch37.rest.ensembl.org'; my $ext = '/ld/human/rs1042779/1000GENOMES:phase_3:KHV?'; my $response = $http->get($server.$ext, { headers => { 'Content-type' => 'application/json' } }); die "Failed!\n" unless $response->{success}; use JSON; use Data::Dumper; if(length $response->{content}) { my $hash = decode_json($response->{content}); local $Data::Dumper::Terse = 1; local $Data::Dumper::Indent = 1; print Dumper $hash; print "\n"; }
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print repr(decoded)
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print(repr(decoded))
require 'net/http' require 'uri' server='https://grch37.rest.ensembl.org' path = '/ld/human/rs1042779/1000GENOMES:phase_3:KHV?' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'}) response = http.request(request) if response.code != "200" puts "Invalid response: #{response.code}" puts response.body exit end require 'rubygems' require 'json' require 'yaml' result = JSON.parse(response.body) puts YAML::dump(result)
import java.net.URL; import java.net.URLConnection; import java.net.HttpURLConnection; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.io.Reader; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://grch37.rest.ensembl.org"; String ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; httpConnection.setRequestProperty("Content-Type", "application/json"); InputStream response = connection.getInputStream(); int responseCode = httpConnection.getResponseCode(); if(responseCode != 200) { throw new RuntimeException("Response code was not 200. Detected response was "+responseCode); } String output; Reader reader = null; try { reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); StringBuilder builder = new StringBuilder(); char[] buffer = new char[8192]; int read; while ((read = reader.read(buffer, 0, buffer.length)) > 0) { builder.append(buffer, 0, read); } output = builder.toString(); } finally { if (reader != null) try { reader.close(); } catch (IOException logOrIgnore) { logOrIgnore.printStackTrace(); } } System.out.println(output); } }
library(httr) library(jsonlite) library(xml2) server <- "https://grch37.rest.ensembl.org" ext <- "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?" r <- GET(paste(server, ext, sep = ""), content_type("application/json")) stop_for_status(r) # use this if you get a simple nested list back, otherwise inspect its structure # head(data.frame(t(sapply(content(r),c)))) head(fromJSON(toJSON(content(r))))
curl 'https://grch37.rest.ensembl.org/ld/human/rs1042779/1000GENOMES:phase_3:KHV?' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'https://grch37.rest.ensembl.org/ld/human/rs1042779/1000GENOMES:phase_3:KHV?' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://grch37.rest.ensembl.org'; my $ext = '/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0'; my $response = $http->get($server.$ext, { headers => { 'Content-type' => 'application/json' } }); die "Failed!\n" unless $response->{success}; use JSON; use Data::Dumper; if(length $response->{content}) { my $hash = decode_json($response->{content}); local $Data::Dumper::Terse = 1; local $Data::Dumper::Indent = 1; print Dumper $hash; print "\n"; }
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print repr(decoded)
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print(repr(decoded))
require 'net/http' require 'uri' server='https://grch37.rest.ensembl.org' path = '/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'}) response = http.request(request) if response.code != "200" puts "Invalid response: #{response.code}" puts response.body exit end require 'rubygems' require 'json' require 'yaml' result = JSON.parse(response.body) puts YAML::dump(result)
import java.net.URL; import java.net.URLConnection; import java.net.HttpURLConnection; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.io.Reader; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://grch37.rest.ensembl.org"; String ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; httpConnection.setRequestProperty("Content-Type", "application/json"); InputStream response = connection.getInputStream(); int responseCode = httpConnection.getResponseCode(); if(responseCode != 200) { throw new RuntimeException("Response code was not 200. Detected response was "+responseCode); } String output; Reader reader = null; try { reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); StringBuilder builder = new StringBuilder(); char[] buffer = new char[8192]; int read; while ((read = reader.read(buffer, 0, buffer.length)) > 0) { builder.append(buffer, 0, read); } output = builder.toString(); } finally { if (reader != null) try { reader.close(); } catch (IOException logOrIgnore) { logOrIgnore.printStackTrace(); } } System.out.println(output); } }
library(httr) library(jsonlite) library(xml2) server <- "https://grch37.rest.ensembl.org" ext <- "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0" r <- GET(paste(server, ext, sep = ""), content_type("application/json")) stop_for_status(r) # use this if you get a simple nested list back, otherwise inspect its structure # head(data.frame(t(sapply(content(r),c)))) head(fromJSON(toJSON(content(r))))
curl 'https://grch37.rest.ensembl.org/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'https://grch37.rest.ensembl.org/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://grch37.rest.ensembl.org'; my $ext = '/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500'; my $response = $http->get($server.$ext, { headers => { 'Content-type' => 'application/json' } }); die "Failed!\n" unless $response->{success}; use JSON; use Data::Dumper; if(length $response->{content}) { my $hash = decode_json($response->{content}); local $Data::Dumper::Terse = 1; local $Data::Dumper::Indent = 1; print Dumper $hash; print "\n"; }
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print repr(decoded)
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print(repr(decoded))
require 'net/http' require 'uri' server='https://grch37.rest.ensembl.org' path = '/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'}) response = http.request(request) if response.code != "200" puts "Invalid response: #{response.code}" puts response.body exit end require 'rubygems' require 'json' require 'yaml' result = JSON.parse(response.body) puts YAML::dump(result)
import java.net.URL; import java.net.URLConnection; import java.net.HttpURLConnection; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.io.Reader; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://grch37.rest.ensembl.org"; String ext = "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; httpConnection.setRequestProperty("Content-Type", "application/json"); InputStream response = connection.getInputStream(); int responseCode = httpConnection.getResponseCode(); if(responseCode != 200) { throw new RuntimeException("Response code was not 200. Detected response was "+responseCode); } String output; Reader reader = null; try { reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); StringBuilder builder = new StringBuilder(); char[] buffer = new char[8192]; int read; while ((read = reader.read(buffer, 0, buffer.length)) > 0) { builder.append(buffer, 0, read); } output = builder.toString(); } finally { if (reader != null) try { reader.close(); } catch (IOException logOrIgnore) { logOrIgnore.printStackTrace(); } } System.out.println(output); } }
library(httr) library(jsonlite) library(xml2) server <- "https://grch37.rest.ensembl.org" ext <- "/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500" r <- GET(paste(server, ext, sep = ""), content_type("application/json")) stop_for_status(r) # use this if you get a simple nested list back, otherwise inspect its structure # head(data.frame(t(sapply(content(r),c)))) head(fromJSON(toJSON(content(r))))
curl 'https://grch37.rest.ensembl.org/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'https://grch37.rest.ensembl.org/ld/human/rs1042779/1000GENOMES:phase_3:KHV?d_prime=1.0;window_size=500' -O -
Methods | GET |
Response formats | json xml jsonp |