Question

How to get a list of snp associated with any known cancer from NCBI with chromosomal locations?

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4.5 years ago

mrj ▴ 170

I am attempting to create human circular genome (using circose) showing a scatter plot of SNPs associated with any known cancer. How can I extract out those SNP information along with chromosome number, location? Thnaks in advance.

SNP Cancer NCBI circos circularGenome • 1.3k views

ADD COMMENT • link updated 4.3 years ago by Ibrahim Tanyalcin ★ 1.2k • written 4.5 years ago by mrj ▴ 170

score 1 · Answer 1 · 2019-10-31

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4.5 years ago

Kevin Blighe 87k

You can download the data from COSMIC: https://cancer.sanger.ac.uk/cosmic/download

Kevin

ADD COMMENT • link 4.5 years ago by Kevin Blighe 87k

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Thank you very much. This is what I wanted

ADD REPLY • link 4.4 years ago by mrj ▴ 170

score 1 · Answer 2 · 2019-10-31

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4.5 years ago

jared.andrews07 ★ 16k

I would likely just download them from a cancer-specific mutation database like COSMIC.

ADD COMMENT • link 4.5 years ago by jared.andrews07 ★ 16k

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Thanks also to Jared.

ADD REPLY • link 4.4 years ago by Kevin Blighe 87k

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Huh, I think you ninja'd me on this one, I didn't see your answer.

ADD REPLY • link 4.4 years ago by jared.andrews07 ★ 16k

score 1 · Answer 3 · 2019-12-22

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4.3 years ago

Ibrahim Tanyalcin ★ 1.2k

6 years ago I've done this tool: http://i-pv.org/ https://github.com/IbrahimTanyalcin/I-PV

here is an example:

http://i-pv.org/1_45/NFKB1

You can get the files as shown here:

ADD COMMENT • link 4.3 years ago by Ibrahim Tanyalcin ★ 1.2k