IndelLDplot

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.

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