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Question: How To Get Chromosome Position Given Rs Number?
0
gravatar for chrismas05
5.3 years ago by
chrismas05 • 0
chrismas05 • 0 wrote:

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
position snp chromosome • 16k views
ADD COMMENT • link •
modified 5.3 years ago by Emily_Ensembl ♦ 17k • written 5.3 years ago by chrismas05 • 0

duplicate of: How to get the chromosome physical position from rs numbers? , Get SNP position from a python interface.

ADD REPLY • link written 5.3 years ago by Pierre Lindenbaum ♦ 116k

I created an iOS app for this exact purpose, I welcome any feedback.

http://chromioapp.com

ADD REPLY • link written 15 months ago by martin.chavez • 0
2
gravatar for karthi.sivaraman
5.3 years ago by
karthi.sivaraman • 30
karthi.sivaraman • 30 wrote:

you can download this information from NCBS dbSNP site. On the other hand, you can also use the SNP-nexus site. Very useful.
ADD COMMENT • link written 5.3 years ago by karthi.sivaraman • 30

Thanks I got it! http://www.ncbi.nlm.nih.gov/projects/SNP/dbSNP.cgi?list=rslist

ADD REPLY • link written 5.3 years ago by chrismas05 • 0

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

ADD REPLY • link modified 8 days ago • written 8 days ago by Shicheng Guo • 7.4k
2
gravatar for Emily_Ensembl
5.3 years ago by
Emily_Ensembl ♦ 17k
EMBL-EBI
Emily_Ensembl ♦ 17k wrote:

BioMart. Help video here.

Use the variation dataset, short variation and indels. Then filter by rsID and choose the position as an attribute.
ADD COMMENT • link written 5.3 years ago by Emily_Ensembl ♦ 17k

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?

ADD REPLY • link written 3.5 years ago by Laura • 20

Use the dedicated GRCh37 Ensembl site.

ADD REPLY • link written 3.5 years ago by Emily_Ensembl ♦ 17k
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