When investgating any SNP, my first port of call woud be the Ensembl Variant Effect Predictor. It uses tools (e.g. sift, polyphen) along with all the Ensembl data to provide the likely consequence or effect of a particular variant. This includes the Ensembl regulatory features and experimentally supported PWM alignments (data from ENCODE, Roadmap Epigenomics etc.) aswell as some miRNA targets and other relevant regulatory regions. It can even tell you whether a particular SNP will improve or decrease the relative binding affinity for a given motif. You can find it online or as a downloadable tool here:

http://www.ensembl.org/tools.html

Since I have worked on such a SNP previously, its a combination of both biochemical tests (activation assays, EMSA, binding studies etc.) and also in silico methods to make a prediction what might bind at this place, if a splice-acceptor site is affected and so on. It usually takes a while to get a complete picture.

Thanks! biochemical analysis of a SNP could be difficult as one has to perform binding assays but can you please explain a bit in silico methods.

I our case the SNP affected a binding site for a transcription factor in an enhancer element. Here we could use it. But you are right, this depends on the situation.

We used tools like TESS and RSAT to analyze the sequences and predict possible binding partners.

As RNA biologist, I believe that in some cases the physiological relevance of SNPs in non-coding regions could be attributed to the function of yet unknown non-coding RNAs, i.e., microRNA, lincRNA, macro long non-coding RNAs, etc. E.g., http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859995/

When investgating any SNP, my first port of call woud be the Ensembl Variant Effect Predictor. It uses tools (e.g. sift, polyphen) along with all the Ensembl data to provide the likely consequence or effect of a particular variant. This includes the Ensembl regulatory features and experimentally supported PWM alignments (data from ENCODE, Roadmap Epigenomics etc.) aswell as some miRNA targets and other relevant regulatory regions. It can even tell you whether a particular SNP will improve or decrease the relative binding affinity for a given motif. You can find it online or as a downloadable tool here:

http://www.ensembl.org/tools.html

I also want to analyse the effect of a SNP in an intron but in the middle of the gene (e.g. intron 6). Do you think that could be due to a change in a transcriptional factor binding site?

Use Human Splicing Finder http://www.umd.be/HSF/ to check whether this change can create alternative splice sites or alter other regulatory sequences. In any case I think the best choice to test the splicing function would be to perform RT-PCR with primers of flanking exons. Good luck!

Thanks every one for their positive contribution, once i also found an insertion of around 250 bases in the intron of the gene. But that region was well known for the insertion deletions. It is also quite interesting to know that why some regions in genome are quite flexible for any change and even some very important genes i.e GJB2 can have mutations very easily.

Also take a peek at these articles:

Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500160/

Characterisation of a functional intronic polymorphism in the human growth hormone (GHI) gene. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500161/

Thanks John Hegarty for suggesting such a nice articles. One more suggestion is http://www.ncbi.nlm.nih.gov/pubmed/22611130.

One easy first step to consider is to see if the SNP falls into a conserved region. If it does, that immediately gives some validation to the finding, which is important because GWAS findings have a tendency to be false positives. The UCSC genome browser, I think, has easily accessed and well developed conservation scores.

Another thing to do would be to blast the vicinity of the SNP against the entire genome, to see if any known regions have matches. Perhaps you have discovered a new target for small RNA hybridization (microRNA and its cousins).

Thanks Andreas Widemuth, its quite interesting to look for microRNA hybridization regions.

Dear all, I find the discussion very interesting and have a following question in this regard. We have a similar situation - candidate gene approach revealed association of a SNP within an intron region of a TF with the mRNA/Protien/Activity of some gene. Now, the question arose - what could be so special with this SNP? But the thing is - we are not sure that this polymorphism which popped up to correlate with mRNA of target gene is the causal one, right? Perhaps, some other linked SNPs which are within the exon regions are of actual matter? Are there any ways to prove it further based on in silico analysis only?

I recommend:

http://regulome.stanford.edu/

Make sure your SNPs are real (as in, you've seen them in your population by sequencing) as many SNPs in dbSNP are not real, but, rather are sequencing errors.

Oh thank you! It looks a very nice site to me, but will this work for the SNP's who are newly identified having no rs number?

No, unfortunately the SNPs have to be in dbSNP and fairly-well characterized for them to be included.

Actually this is the problem when we have some new change how can we label it or in a single go come to know that it will have some effect or not on gene function.

We have just described an interesting mechanism by which intronic SNPs influence gene expression, the article is free at

http://www.nature.com/articles/srep18741

I am having the same situation and found this discussion very interesting and helpful. thank you all for the positive contributions.

Regarding intronic SNPs, it almost is associated with regulatory features according to its location, e.g. if it near to intron-exon junction, it is prone to affects the splicing process and interrupt the splicing factors either enhancer or silencer SF. If it near to the middle of an intronic region, it is prone to affect the TF binding site for the neighboring gene. so according to SNP location inside the intron, your attention will be guided to the proper algorithm used.