Making Linkage Disequilibrium blocks from SNPs position for NCBI Build 38

Question

[Bahar]

Hello evryone

I'd like to know if anyone has or might know how can I make LD block from my SNPs list for the last human genome build (GRCh38). I'm currently working on the GWAS Iranian population. I'm trying remove high LD regions from my dataset in QC prosses.

I using of plink r2 command for finding connected SNPs. but I can't find the best way for estimating region LD blocks!

anyone can help me

Thanks a lot in advance for the attention!

Answer 1

[Denise CS]

Have you checked the LD data in Ensembl e.g. rs1333049. This is the plot for that variant and help on the Linkage disequilibrium data is also available.

Answer 2

[reza.jabal]

If you are carrying out a GWAS in Iranian population you have to select your tag SNPs from the same population, otherwise you introduce population stratification bias into your data! This means that you cannot select your tag SNPs from the reference population and then genotype your samples at those loci!

Answer 3

[chrchang523]

The plink --blocks command is designed for this.