I'm trying to identify gene names for the list of SNP (GWAS result) and have some inconsistencies. For some SNPs gene names were identified using BioMart package in R (by BP - if it is located inside the gene and #chr - the same as gene). For these SNPs I make a plot in LocusZoom and get a list of genes. And not always gene which was identified with BioMart is included in the list of genes from LocusZoom.
Could you please explain, what is the reason of this inconsistencies? And can I consider genes identified by BP and chr# using BioMart correct?