Question: How To Determine The Effect A Snp On The Expression Of The Gene
gravatar for win
6.5 years ago by
win810 wrote:

Hi all, i have a list of SNPs for a gene. I want to know if there is a way to determine the effect of each of the SNPs on the expression of that gene.

Thanks in advance.

snp • 4.9k views
ADD COMMENTlink modified 6.5 years ago by swbarnes26.7k • written 6.5 years ago by win810
gravatar for munch
6.5 years ago by
munch300 wrote:

Here is a similar post: Anyone know a *general* variant (SNP/indel) effect predictor / annotator?

For this I used snpEff ( which provides variant annotation and effect prediction. As input you can use your SNP list in vcf format (

Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF). Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.


java -Xmx4g -jar snpEff.jar eff -v GRCh37.66 file.vcf > file.eff.vcf

see here for installation guide and examples:

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by munch300
gravatar for Anthony Mathelier
6.5 years ago by
University of Oslo, Oslo, Norway
Anthony Mathelier870 wrote:

It seems you are more interested in the effect on the expression. Hence you should focus on the regulatory regions. Have a look at regulomeDB then (

ADD COMMENTlink written 6.5 years ago by Anthony Mathelier870
gravatar for swbarnes2
6.5 years ago by
United States
swbarnes26.7k wrote:

If only biology were that simple...

As a rule, no, there is not totally in silico way to predict that. You would have to see if someone has empirically tried to correlate SNPs in that approximate position with expression. This might be feasible in a species like mice, where the genetics are a bit simpler, since the mice come from inbred strains.

I suppose you could try and see if your SNPs sits on a known regulation site, and how much your SNPs changes that site from the canonical consensus sequence.

But if you are looking for a simple function where you put your SNP in, and biological consequences like expression changes come out, no, that doesn't exist.

ADD COMMENTlink written 6.5 years ago by swbarnes26.7k
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