why distance limit for pairwise LD calculation is 500K in SNAP ?

Question

[sinorenjianyi]

https://www.broadinstitute.org/mpg/snap/ldsearchpw.php

Do we assume two SNPs further than 500Kbp from each other are in LE？

[Fabio Marroni]

They are not necessarily in LE, but it is true that at increasing distance LD decays, and if distance is great LD tends to be very low. In addition, I think there were computing time issues there. LD is computed between all possible pairs of SNPs. If in a chromosome you have 10000 SNPs, you need to perform 100009999/2 4.99510^8 comparisons. If only 1000 SNPs are closer than 500kb you "only" need 1000999/2, i.e. 4.99510^6 comparisons. Given that SNPs far from one another are quite a lot and that they are usually not in LD, here you havve the motivation!

Answer 1

[sinorenjianyi]

https://www.broadinstitute.org/mpg/snap/faq.php#whyismaxdistancelimit found the official explanation

And there is indeed a database for long range LD http://www.ncbi.nlm.nih.gov/pubmed/19878600