I was annotating my dataset with biomart with filtering by chromosomal region and was surprised by the genes I got, so I took a closer look on PRAMENP (ENSG00000197549).
According to biomart its positions are:
but if I look at genome browser I get following:
GENCODE Transcript Annotation ENST00000337471.4 (PRAMENP)
|HAVANA manual id||OTTHUMT00000320276.2||OTTHUMG00000150836.3|
because of those differences while using biomart I get lots of genes that are far away from my dataset (SNPs) according to genome browser. And those that are really close to them (according to genome browser) do not appear in biomart.
ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org",
filterlist = list("22:21815836:22006492")
attributes.1 = c("chromosome_name","start_position", "end_position","strand", "ensembl_gene_id", "hgnc_symbol")
results.1 = getBM(attributes = attributes.1, filters = c("chromosomal_region"), values = filterlist, mart = ensembl)> unique(results.1$hgnc_symbol)
 "PRAMENP" "MAPK1" "" "TOP3B" "PPM1F"
But according to genome browser (coordinates: chr22:21,815,836-22,006,492) I should have got UBE2L3,YDJC, PI4KAP2 and some more but not those identified by biomart.
I guess the biomart dataset is build on hg38, and I am viewing hg19 in genome browser. Is it possible to get hsapiens_gene_ensembl in hg19?