[BioC] How to get a unique line of annotation for each specific genomic position by using biomaRt package

[Mao Jianfeng]

Dear listers,

I am new to bioconductor.

I have genomic variations (SNP, indel, CNV) coordinated by
chromosome:start:end in GFF/BED/VCF format. One genomic variation is
defined a specific genomic position (in base pair).

for example:
# SNPs,chr,start,end
SNP_1,1,43,43
SNP_2,2,56,56

I would like to get such genomic variations annotated by various
gen/protein/passway centric annotations (as listed in BioMart
databases). I tried R/bioconductor biomaRt package. But, I failed to
get a unique line of annotation for a specific genomic position. Could
you please give any directions on that?

Thanks in advance.
################################################code I used as an
example###########################
library(biomaRt)
listMarts()
plant = useMart("plant_mart_7")
alyr=useDataset("alyrata_eg_gene", mart=plant)
atha = useDataset ("athaliana_eg_gene",mart=plant)

listAttributes(alyr)
listFilters(alyr)

chr<-c(rep(1, 10))
start<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000)
end<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000)

getBM(attributes =
c("chromosome_name","start_position","ensembl_gene_id",
"go_biological_process_linkage_type"), filters = c("chromosome_name",
"start", "end"), values = list(chr, start, end), mart=alyr, uniqueRows
= TRUE)
###########################################################################################



-- 
Jian-Feng, Mao