Try Homer annotate peaks with your custom annotation file (gff3).

http://homer.ucsd.edu/homer/ngs/annotation.html

You can use BEDOPS bedmap and gff2bed to map TAIR10 annotations (or annotations from any reference genome you have a GFF file for) to ChIP-seq peaks, i.e.:

$ bedmap --echo --echo-map peaks.bed <(gff2bed < annotations.gff) > answer.bed

If you don't need the entire annotation, you can use --echo-map-id or other --echo-map-* options to get a subset of the annotation data. See the documentation or bedmap --help for more detail.

Can it be happening, because in my bed file i have chromosom name strating with lower case and in the reference genome with upper case?

You can also annotate your peaks using a simple closestBED -a peaks.bed -b genes_with_coordinates_annotation.bed

This would allow you to annotate your peaks with any coordinate-description (gene, CTCF site, etc..) file.