Colocalization analyses assess the degree to which independent signals of association,
including eQTL and GWAS signals, share the same causal variant. In cottonMD, user can make full use of RNA-seq
data in cottonMD to perform colocalization analyses by uploading user’s phenotype datasets. Colocalization
analyses in cottonMD was performed using COLOC R package.
Summary of colocalisation analysis (the number of SNPs
analysed and the posterior probabilities of H0, H1, H2, H3 and H4)
H0: neither trait has a genetic association in the region
H1: only trait 1 has a genetic association in the region
H2: only trait 2 has a genetic association in the region
H3: both traits are associated, but with different causal variants
H4: both traits are associated and share a single causal variant