Linkage disequilibrium after HapMap

Question

[Kizuna]

Dear All,

After shutting down HapMap, I am finding some difficulties to assess the L.D between SNPs.. any suggestion about an alternative browser is welcomed ..

Thx

[Kevin Blighe]

Hi Kizuna, what do you mean by 'shutting down HapMap'? Also, to which 'browser' are you referring?

Kevin

Answer 1

[Pramod Shinde]

The automatic choice is Plink.

Answer 2

[Maki]

For simple lookups, see here (based on 1000 Genomes)

https://ldlink.nci.nih.gov/?tab=ldmatrix