PExFInS

The generation of Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) was originated from the observation that high proportion of cis-acting expression quantiative trait loci (cis-eQTLs) emerged in GWAS SNPs and the underexplored status of indel cis-eQTLs for GWAS. We believe that the integration of cis-eQTLs, especially indel cis-eQTLs, with candidate disease-associated variants generated from GWAS could facilitate the identification of causal genes or disease mechanisms. On the other hand, the biological information encoded in human genome, such as regulatory features from the Ensembl regulatory database, will be conductive in pinpointing functional causal variant(s) for the disease association. Thus, we generated a pipeline, PExFInS to integrate our LCL cis-eQTL data, along with publicly available cis-eQTL datasets derived from lung tissues, human monocytes, dendritic cells, blood, and LCLs.

Features

Linkage disequilibrium (LD) analysis with genotyping data of SNPs and indels from the 1000 Genomes (1KG) Project, including the Phase I release (1092 individuals) and the Phase III release (2504 individuals).
Compare LD pattern of query variants, including indels and SNPs, among all populations included in the 1KG Project
cis- or trans-acting expression quantitative trait loci (eQTL) analysis among 423 LCLs on 6 global populations, including CHB, JPT, CEU, MEX, LWK and YRI
Comprehensive annotation for these high LD variants, including indels and SNPs, with ANNOVAR
Ensembl Regulatory Region mapping for these high LD vairants.
cis-eQTL mapping with other already published cis-eQTL datasets.
Automatically search these high LD variants in the GWAS Catalog.
Generate final annotation for these high LD variants in pretty HTML file with annotation links.
Provide UCSC custom track for visulization of LD pattern, cis-eQTL result, and overlapped Ensembl regulatory regions.
Generate LCL eQTL plot for interested variants among six populations, including CHB, JPT, CEU, MEX, YRI, and LWK.