GWAS Mapping Precision

This tool is designed to quantify the physical distance, linkage disequilibrium (LD) and difference in minor allele frequency (MAF) between the top associated SNPs identified from GWAS and the underlying causal variants. The results are from simulations based on whole-genome sequencing data (Wu et al. 2017). Shown is proportion of the GWAS top SNPs of which the corresponding causal variants are within a certain distance, LD and/or MAF difference threshold as specified in the options below.

Please specify the thresholds

Citation: Wu et al. (2017) Quantifying the mapping precision of genome-wide association studies using whole-genome sequencing data. Genome Biology, 18(1): 86.

Credits: Zhili Zheng, Yang Wu and Jian Yang at the Program in Complex Trait Genomics, The University of Queensland

Troubleshooting: Jian Yang


Note:
WGS: GWAS using whole genome sequencing data.
1KPG3: GWAS using SNP array data imputed to 1KGP Phase 3.
1KPG1: GWAS using SNP array data imputed to the 1000 Genome Project (1KGP) Phase 1.
HAPMAP2: GWAS using SNP array data imputed to the HapMap Project Phase 2.