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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