Annotate noncoding regions for 1000 genome data

Question

[qwzhang0601]

Is there any tool or database to annotate the SNPs in the noncoding regions? I am working on 1000 genome data. Usually there are clear annotation for exotic SNPs. But I also interested those SNPs which are in functional elements located in noncoding regions (e.g. enhancer, TFBS). I found most databases are tissue and cell specific, so I wonder whether there are such annotation database for 1000 genome data. I think the tissue of 1000 genome samples is blood, but not sure about the cell line.

Thanks

Answer 1

[Denise CS]

Use the Variant Effect Predictor (aka VEP) to annotate your variants, whether they are in coding regions or otherwise. By using the VEP you will also find out whether you variants map to a TFBS or regulatory element. This regulatory annotation is as a result of The Ensembl Regulatory build. There is an incredibly wealthy of Output options for anyone to choose from. There is a VEP script if you know Perl but if you rather use another language than Perl have a look at the variation endpoints in the Ensembl REST API. And of course, the web interface of the VEP.

[qwzhang0601]

Thank you for your suggestion

Answer 2

[EagleEye]

I hope this will help you somehow.

SNP-nexus:

http://snp-nexus.org/about.html

http://snp-nexus.org/index.html

lncRNASNP:

http://bioinfo.life.hust.edu.cn/lncRNASNP/

http://bioinfo.life.hust.edu.cn/lncRNASNP/download

[qwzhang0601]

I will take a look at them. Thanks