###  ASSOCIATION ANALYSIS with Transferrin  Phenotype ###

plink --bfile Transferrin --pheno Tr.pheno --maf 0.05 --geno 0.01 --hwe 0.001 --assoc --out GWAS_T_add


###  ASSOCIATION ANALYSIS with Height Phenotype ###

plink --bfile Transferrin --pheno Ht.pheno --maf 0.05 --geno 0.01 --hwe 0.001 --assoc --out GWAS_H_add



### LD of top association SNPs (obtained using the R script for the PLINK association analysis results) for Transferrin and Height  ###

plink --bfile Transferrin --extract SNPlistTransferrin.txt --r2 --out LD_T_Subset


plink --bfile Transferrin --extract SNPlistHeight.txt --r2 --out LD_H_Subset