I am querying 1KG based on hugo ID, and I noticed that, for some of the genes, there are several entries with different ensemble ID. I appreciate if someone can make comments on that, for example, if you look into CFB in the 1KG, (click here) several different ensemble id are assosiated to this Hugo ID. I hope that I had phrased my question properly.
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User 1933 •
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this most likely happens when alternate sequence assemblies exist. The ensembl id ENSG00000243649 identifies CFB on the primary assembly while ENSG00000204359 identifies CFB on some alternate assembly. Have a close look at the location information provided (Chromosome 6: 31,895,475-31,919,861 vs. Chromosome HSCHR6_MHC_MANN: 31,952,850-31,957,964).
For more information about alternate sequence assemblies in ensembl check this post.
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