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Assuming I have SNPs data using hg19, how can I know which SNP belongs into which Gene?

The data looks like:

chr10_103577643
chr10_124712463

and so on.

I want to add a column of Gene, which would tell to which Gene the SNP belongs. The file is not a VCF file but a Txt file.

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    $\begingroup$ Please edit your question and show us an example of your data. What do you have? A list of rsIDs? A VCF file? Some other format? How many SNPs? $\endgroup$
    – terdon
    Jul 9 '18 at 8:22
  • $\begingroup$ Just annotate the vcf file. $\endgroup$
    – arup
    Jul 9 '18 at 12:10
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Use the Variant Effect Predictor(VEP)

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  • $\begingroup$ Please don't just post links as answers. It would be great if you could add a short explanation of what VEP is, how to use it etc. Otherwise, this is really a comment and not an answer and would become useless in the (admittedly unlikely) case where the VEP were to be discontinued or its URL changed. For instance, pasting chr10_103577643 into VEP doesn't work, so you could explain what format the data would have to be in. $\endgroup$
    – terdon
    Jul 15 '18 at 13:02
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You can use snpEff or snpSIFT java annotator also for hg19.

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  • $\begingroup$ Please don't just post links as answers. It would be great if you could add a short explanation of these tools do, how to use them etc. Otherwise, this is really a comment and not an answer and would become useless if the tools were to be discontinued or their URLs changed. $\endgroup$
    – terdon
    Jul 15 '18 at 13:03

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