<p>Use the <a href="http://grch37.ensembl.org/info/docs/tools/vep/index.html" rel="nofollow noreferrer">Variant Effect Predictor(VEP)</a></p>

CC BY-SA 4.0
2018-07-15T13:02:34.720Z
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.
terdon
CC BY-SA 4.0
2018-07-09T07:47:20.313Z
2018-07-09T07:47:20.313Z
Emily_Ensembl
<p>You can use <a href="http://snpeff.sourceforge.net/SnpEff_manual.html" rel="nofollow noreferrer">snpEff</a> or <a href="http://snpeff.sourceforge.net/SnpSift.html" rel="nofollow noreferrer">snpSIFT</a> java annotator also for hg19.</p>

CC BY-SA 4.0
2018-07-15T13:03:19.677Z
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.
terdon
CC BY-SA 4.0
2018-07-09T08:21:43.623Z
2018-07-09T08:21:43.623Z
Andrea Spinelli
<p>Assuming I have SNPs data using hg19, how can I know which SNP belongs into which Gene? </p>

<p>The data looks like:</p>

<pre><code>chr10_103577643
chr10_124712463
</code></pre>

<p>and so on. </p>

<p>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. </p>

CC BY-SA 4.0
2018-07-09T08:22:23.773Z
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?
terdon
CC BY-SA 4.0
2018-07-09T12:10:10.253Z
Just annotate the vcf file.
arup
<gene><snp><hgp>
Associating SNP and GENE
# Associating SNP and GENE

(Asked by: username_0 on 2018-07-08)

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.

**Tags:** gene, snp, hgp
> **Comments:**
> **username_1**: 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?  
> **username_2**: Just annotate the vcf file.  

---

## 2 answers

### Answer by username_3 on 2018-07-09. Score: 3

Use the [Variant Effect Predictor(VEP)](http://grch37.ensembl.org/info/docs/tools/vep/index.html)

> **Comments:**
> **username_1**: 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.  

---

### Answer by username_4 on 2018-07-09. Score: 2

You can use [snpEff](http://snpeff.sourceforge.net/SnpEff_manual.html) or [snpSIFT](http://snpeff.sourceforge.net/SnpSift.html) java annotator also for hg19.

> **Comments:**
> **username_1**: 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.  

---

