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.

Project Activity

See All Activity >

Follow IndelLDplot

IndelLDplot Web Site

Other Useful Business Software

Gen AI apps are built with MongoDB Atlas

The database for AI-powered applications.

MongoDB Atlas is the developer-friendly database used to build, scale, and run gen AI and LLM-powered apps—without needing a separate vector database. Atlas offers built-in vector search, global availability across 115+ regions, and flexible document modeling. Start building AI apps faster, all in one place.

Start Free

Rate This Project