text: user8875: I have 3 SNPs that are in LD in 'several' populations here:
  https://www.ebi.ac.uk/gwas/variants/rs13078854#ld_panel_label
  It's a pain to look at all (30) populations one by one to manually check if the 3 SNPs are in LD in a given population or not.
  Is there a way to ask this question more systematically? e.g. in which common imputation populations are a given set of SNPs in LD (above a certain threshold)?
  
  user3848: There is a risk of a type 2 error.
  My advice would be to use Structure if it is still available given the situation. Its not great and it is old and its a GUI and I don't know whether it has been updated (I'm not exactly selling this am I?), but it will do the job of navigating through a type 2 error.
  What you do is provide the number of populations a priori and it will assign a Bayesian estimate of HW equilibrium for that number of populations. You manually input 1,2,3,4,.... 30 run and wait. The point at which the joint marginal plateaus is the minimum number of populations which do not exhibit LD (thus if two of your populations exhibit LD it collapse them into one). Thus if your answer is '20' it give some confidence it is a real result. If it is like 10 (optimistically) the conclusion would be in pretty reasonable shape.
  There are other ways of looking at this, but that would be my starting point.
  The classic calculation is LDHat, here https://github.com/auton1/LDhat, but the last update was 2015 and in this particular circumstance I'm not sure.
  
original_text: 8875: <p>I have 3 SNPs that are in LD in 'several' populations here:
  <a href="https://www.ebi.ac.uk/gwas/variants/rs13078854#ld_panel_label" rel="nofollow noreferrer">https://www.ebi.ac.uk/gwas/variants/rs13078854#ld_panel_label</a></p>
  <p>It's a pain to look at all (30) populations one by one to manually check if the 3 SNPs are in LD in a given population or not.</p>
  <p>Is there a way to ask this question more systematically? e.g. in which common imputation populations are a given set of SNPs in LD (above a certain threshold)?</p>
   3848: <p>There is a risk of a type 2 error.</p>
  <p>My advice would be to use <code>Structure</code> if it is still available given the situation. Its not great and it is old and its a GUI and I don't know whether it has been updated (I'm not exactly selling this am I?), but it will do the job of navigating through a type 2 error.</p>
  <p>What you do is provide the number of populations <em>a priori</em> and it will assign a Bayesian estimate of HW equilibrium for that number of populations. You manually input 1,2,3,4,.... 30 run and wait. The point at which the joint marginal plateaus is the minimum number of populations which do not exhibit LD (thus if two of your populations exhibit LD it collapse them into one). Thus if your answer is '20' it give some confidence it is a real result. If it is like 10 (optimistically) the conclusion would be in pretty reasonable shape.</p>
  <p>There are other ways of looking at this, but that would be my starting point.</p>
  <p>The classic calculation is LDHat, here <a href="https://github.com/auton1/LDhat" rel="nofollow noreferrer">https://github.com/auton1/LDhat</a>, but the last update was 2015 and in this particular circumstance I'm not sure.</p>
  