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.
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.