I'm new to this field and first time posting, please bear with me.
I am working on locating the functional effects of SNPs which appear to be relevant in our candidate gene study. I am aware of individual websites such as miRanda, TRANSFAC, ESE-finder etc that can help predict miRNA binding sites, TF binding sites and exon splicing elements. However, with a long list of SNPs to search, (eg. 100 or more), it is quite a pain to search each individual site with 1 SNP at a time.
Is there a meta-tool that someone can recommend which allows easy input (rs# only) and combines many functional options?
I have already tried some tools, many of which are no longer working - F-SNP, Pupasuite, SNPit etc, Amongst the others that have given me some results, SNP Function Portal, SNPinfo and pfSNP, I am having trouble 'trusting' them since all of these sites have given me different answers (such as TFs) for the same SNP I tested.
If anyone has some insights, I would be very grateful! Thanks for your patience.