SNP Proxy dataset
Hello, I'm new to this major, and I have a question. Where can I get available data for SNP Proxy like the result form Proxy Search in http://archive.broadinstitute.org/mpg/snap/ldsearch.php
I have searched for it but no luck. I found that Ensenbl they have something awesome like this: http://www.ensembl.org/Homo_sapiens/Variation/HighLD?db=core;r=7:24926327-24927327;v=rs123;vdb=variation;vf=119#373508_tablePanel from this post Pre-computed list of genes in LD with a SNP with r2 from 1000Genomes / hg19 .
But unlucky, I can not use the Ensembl API for my task. Is there a way to calculate this using public dataset from Ensembl or any others resource.
Many thanks !!!
• 5,035 views
•
link
written
by
robust1308 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How assign PAR regions to X or Y for an rsID in VCF?
written by magnolia •
-
Obtaining variant allele frequencies with the Ensembl API
written by robles.daniela
-
Allele discrepancy between Database and Publication
written by snp_guy •
-
biomaRt and gprofiler not mapping rsid's that exist on ensembl site
written by bdarius85 •
-
Why there are some discrepancies between VEP output and "variation" section of Ensembl?!
written by seta
-
Obtain the LD matrix from a list of SNP
written by janhuang.cn
-
Finding homozygotes with SNP of interest
written by andrey.v.shubin
-
1000 genomes, meaning of the color of pie charts for population genetic
written by bzhtgb •
-
detecting SNP allele and genotype frequencies from 1000 genomes at ensembl
written by Viktor Bojovic •
-
Sanger sequencing results don't match the reference and alt alleles?
written by maddie.hughes •
Try LDlink, haploreg ?
Hello, zx8754, Thank for your information, but I intent to write a python script that take Ensembl or others source and output is SNP Proxy.
We can download the data from haploreg - http://archive.broadinstitute.org/mammals/haploreg/data/