How To Get Chromosome Position Given Rs Number?
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8.6 years ago
chrismas05 • 0

I have a list of a few hundred SNPs given by rs number. I want to get the chromosome and position for each SNP. For example:

input: rs4477212 output: chr1:82154

snp chromosome position • 25k views
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I created an iOS app for this exact purpose, I welcome any feedback.

http://chromioapp.com

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8.6 years ago

you can download this information from NCBS dbSNP site. On the other hand, you can also use the SNP-nexus site. Very useful.

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SNP-nexus is quite good. However, when the rs number > 20000, it will become very slow...

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8.6 years ago
Emily 23k

BioMart. Help video here.

Use the variation dataset, short variation and indels. Then filter by rsID and choose the position as an attribute.

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Hello Emily,

I have a data file for imputation only with rs numbers and my referecence vcf file has rsnumber:Chro:position:allele1:allele2.

Biomart has the H. sapiens variation in GRCh38 and my ref. file (1KG) is in GRCh37. How could I proceed?

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Use the dedicated GRCh37 Ensembl site.

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