Thank you

please also have a look at

http://compbio.cs.queensu.ca/F-SNP/ is a functional database for snps, while this https://rostlab.org/services/snap2web/ tool provides functional effect prediction.https://www.regulomedb.org is another great source also, usually used with Haploreg to mine ENCODE database.

http://fitsnps.stanford.edu/(Functionally interpolated SNPs; http://fitsnps.stanford.edu/)  provides a new way to distinguish disease-associated genes from false positives in genome-wide association studies. The feature is based on human microarray data, and it reveals the association between gene expression and disease-associated variants.but if we have a vcf files we may use http://variant.bioinfo.cipf.es/

Thank you, 

I found both Haploreg and F-SNP very useful!