Hi experts, Is there any bioinformatics software that can predict any common CNV or coding SNP in LD with an other intronic SNP?

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James Lee

Try SNAP - easiest to find by googling "SNAP SNP". It can provide proxies for most SNPs at varying levels of LD. Be careful though, just because there may be a coding variant in LD, doesn't mean that is the causal SNPS.

Evangelos Evangelou

SNAP was a great tool but stopped being updated about a year ago. LD is calculated with 1KG phase 1 data. I would try SNiPA instead, which use the latest reference panels from 1KG project.