Hello!
I am trying to find SNPs which are in linkage disequilibrium with my target SNP on LDproxy (https://ldlink.nci.nih.gov/?tab=ldproxy), however I realize I get very different results using different genome builds (hg37 and hg38). In particular, one interesting LD SNP result I got for hg37 completely disappeared for hg38. The SNP can still be found on hg38 ENSEMBL.
I do not think the query region has been removed or changed from hg37 to hg38, and I would really appreciate any explanation regarding the vast differences in results for hg38 and hg37.
Thank you and have a great day! :)
Hi Kay
some changes have been done during evolutions of the human genomes assemblies. in the last genome all sequences are now published and therefore some position have changed.
just go to the UCSC genome browser (http://genome.ucsc.edu), search for your genes or region of interest, choose the CHM13 version of the genome and open the optional track named "cactus alignment" to get an idea on what happened.
maybe it's just a problem of positions, you must use the rsid prior to their positions.
all the best
fred
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