Functional Epigenetic Annotation Tool of SNPs (FeatSNP) is an online tool and a curated database for exploring common SNPs' potential functional impact on the human brain. FeatSNP currently supplies the following functional and epigenetic annotations of human SNPs:
*Transcription Factors (TFs) binding potential:
We predicted the Transcription Factors (TFs) binding potential within 21bp DNA sequences surrounding each SNP by using the Position Weigh Matrix of 519 vertebrate TFs. Meanwhile, we estimated the binding affinity changes of TFs in the context of SNP alleles switching.
*Expression correlation between the SNP-associated gene and SNP-associated TFs:
By using 1,259 transcriptome datasets from 13 brain tissues, we calculated the expression correlation coefficient (Pearson) between the SNP-associated gene and the transcription factors that were predicted to bind to the SNP in 13 brain regions (1259 samples).
*eQTL information:
We provided the eQTL information of SNPs in 10 brain regions.
*Epigenomic modification around SNPs:
We visualized the epigenetic landscape around SNPs by using an epigenome browser. Topologically-Associating Domains (TADs) information was included to understand the connection between SNPs and nearby genes.
Currently, FeatSNP hosts the brain-specific functional and epigenetic annotations of 81M SNPs in the human genome.