I am using this UCSC genome browser to do some functional annotation on the top SNP and its high LD SNPs. And would like to know the chromatin state segmentation.
My top SNP is located in the intergenic region of GENE1 and GENE2. From the UCSC chromatin data is seems like both these genes are located in the active promoter regions. While my top SNP locus is located in the Strong enhancer region.
My question is, if my top SNP locus is a strong enhancer how would I know - which gene (GENE1 or GENE2) it has effect on (i.e. Enhance the gene expression)
Is there something like the closest gene to the topSNP has more effect!!?