How far from the SNP may the causative genes be?

Aharon Brodie, Johnathan Roy Azaria, Yanay Ofran

Research output: Contribution to journalArticlepeer-review

111 Scopus citations


While GWAS identify many disease-associated SNPs, using them to decipher disease mechanisms is hindered by the difficulty in mapping SNPs to genes. Most SNPs are in non-coding regions and it is often hard to identify the genes they implicate. To explore how far the SNP may be from the affected genes we used a pathway-based approach. We found that affected genes are often up to 2 Mbps away from the associated SNP, and are not necessarily the closest genes to the SNP. Existing approaches for mapping SNPs to genes leave many SNPs unmapped to genes and reveal only 86 significant phenotype-pathway associations for all known GWAS hits combined. Using the pathway-based approach we propose here allows mapping of virtually all SNPs to genes and reveals 435 statistically significant phenotype-pathway associations. In search for mechanisms that may explain the relationships between SNPs and distant genes, we found that SNPs that are mapped to distant genes have significantly more large insertions/deletions around them than other SNPs, suggesting that these SNPs may sometimes be markers for large insertions/deletions that may affect large genomic regions.

Original languageEnglish
Pages (from-to)6046-6054
Number of pages9
JournalNucleic Acids Research
Issue number13
StatePublished - 27 Jul 2016

Bibliographical note

Publisher Copyright:
© 2016 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.


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