Snp Function Explaination In Intergenic Region

Question

[J.F.Jiang]

Hello, everyone!

I recently collected some SNPs related with one disease. LD calculation for SNP expansion has been done; I found lots of SNPs are mapped to intergenic regions.

From knowledge of GWAS references, SNPs in this region can indeed also regulate gene expression. But so far I have not found any SNP annotation database or sysmatic explaination of this kind of SNPs. Could anyone here share their point of how to do this work?

Also, some papers mentioned the database of lincRNA including miRNA and >200bp RNA region, but still I have not found any entries for a database (Ensembl mentioned in gene annotation, but I cannot find the entries). Could anyone offer your kind help?

Anyway, thanks a lot!

Answer 1

[Sander Timmer]

It might be useful if you gave some examples about the SNPs you're looking at....

Using Ensembl you can actually look in quite some detail at the LD structure around this specific SNP (or location) and see what other SNPs are within what recombination distance. Also, within Ensembl you could load different tracks of known phenotypic data from Encode for example to study what your SNP could be involved in.

What kind of database are you hoping to find? Or what specific feature of a SNP are you looking for?

[J.F.Jiang]

sorry, maybe i did not clearly clair about my doubt. I want to have a look at a database which some annoatations for intergenic have been offered, that is like ucsc, start point, end point, regulatory element and something like this!

Answer 2

[mulin0424.li]

Recent tools and databases on this level:

HaploReg: http://www.broadinstitute.org/mammals/haploreg/haploreg.php

RegulomeDB: http://regulome.stanford.edu/

GWAS3D: http://jjwanglab.org/gwas3d

Answer 3

[User 1940]

SNP annotation database? You mean something like NCBI dbSNP? There you can filter for intergenic SNPs.

http://www.ncbi.nlm.nih.gov/projects/SNP

What is the disease (or phenotype) that you have those SNPs for? There may be disease-specific databases out there.

PS. Check out this thread as well, it may be helpful: Analysis Of Snps In Gene Deserts

[J.F.Jiang]

Thank you for your quick answer. I am not looking for a general database like dbsnp. i want to download the annotation file for intergenic region, or lincrna annotation!

Answer 4

[Pablo]

I don't know if it's exactly what you mean, but may be something like this can help:

ftp://ftp.ensembl.org/pub/release-63/regulation/homo_sapiens/AnnotatedFeatures.gff.gz

Answer 5

[Larry_Parnell]

You are likely to find very little functional annotation of intergenic regions, let alone compiled into a database.

Annotation of genomic features is more easily obtained from a standard genome browser - such as UCSC or Ensembl.

For tools to analyze the deleterious nature of SNPs in DNA, see Table 2 in Cooper and Shendure's paper (Nature Reviews Genetics 12:628-640):

phastCons http://compgen.bscb.cornell.edu/phast/
GERP http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html
Gumby http://pga.jgi-psf.org/gumby/
phyloP http://compgen.bscb.cornell.edu/phast/
SCONE http://genetics.bwh.harvard.edu/scone/
binCons http://zoo.nhgri.nih.gov/binCons/index.cgi
Chai http://research.nhgri.nih.gov/software/chai
VISTA http://genome.lbl.gov/vista/index.shtml