Over the past decade, genome-wide association studies (GWAS) have been widely used to identify disease associated gene loci. However, the majority of the identified variants are in noncoding regions, making it difficult to identify functional variants and eventually actionable drug target gene/protein. Our newly released GeneticsLand can help to accelerate identification of drug target with its powerful ability to integrate variant annotation, associated eQTL and association study results.
Here is an example of how GeneticsLand quickly identify potential associated genes of noncoding variants identified in a research article on inflammatory bowel disease (IBD) (1)
In this article, the author investigated 4734 variants from 152 IBD associated GWAS loci and identified 18 prioritized noncoding SNPs that may contribute to IBD by regulating nearby genes.
Having the list of noncoding SNPs, GeneticsLand can help to quickly research SNP annotation, association, eQTL and more.
1. GeneticsLand allows user access to annotation information from a variety of resources without using each of the individual annotation tools:
2. GeneticsLand integrates phenotype association information from published research articles. It allows users to research other phenotypes associated with the SNP of interest. In this example, SNP rs2231884 is shown to be associated with IBD in a Nature article from 2012, reinforcing the finding in the original article.
3. GeneticsLand helps user to research eQTL information, which may lead to discovery of new associated genes. For example, in the original article, the author identified CCDC85B, FIBP and FOSL1 as nearby genes and suggests the SNP may contribute to IBD pathogenesis by regulating nearby genes. However, none of these genes was known to be associated with IBD or any immunological related pathways. By using GeneticsLand, we found that SNP rs2231884 has an eQTL association with a couple of genes, including CTSW, which encodes a cysteine proteinase that may have a function regulating T-cells cytolytic activity.
(1). Mesbah-Uddin, Md, Ramu Elango, Babajan Banaganapalli, Noor Ahmad Shaik, and Fahad A. Al-Abbasi. "In-Silico Analysis of Inflammatory Bowel Disease (IBD) GWAS Loci to Novel Connections." PloS one 10, no. 3 (2015): e0119420.