Lets say these are the binding sites of MotifX:

chr2    70258563    70258573
chr2    70277815    70277825
chr2    113996917    113996927

I want to see if they are closer to a centromeric or telomeric region.
How can I calculate genomic region preference to be closer to a centromere/telomere?

My solution is this:
Here we can get Easiest Way To Obtain Chromosome Length? and centrome position
(curl -s "ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz" | gunzip -c | awk 'BEGIN {OFS="\t"}; ($2=="chr2" && $8=="centromere") {print $2,$3,$4}').

length: chr2 243199373
position: chr2 92326171    95326171

From this we can make chromosome map:

Telomere region A = [1 ; 92326171/2]
Centromere region = [92326171/2 ; 95326171+((243199373-95326171)/2)]
Telomere region B = [95326171+(243199373-95326171)/2 ; 243199373]

  1------//------46163085------//------169262772------//------243199373
     TelemoreA             Centromere              TelemoreB
      region                region                  region

And a BED file:

cat chromosome_map.bed
chr2    1            46163085     Telomere_region
chr2    46163086     169262771    Centromere_region
chr2    169262772    243199373    Telomere_region

intersectBed -a MotifX_bs.bed -b chromosome_map.bed -wo
chr2    70258563    70258573    chr2    46163086    169262771    Centromere_region    10
chr2    70277815    70277825    chr2    46163086    169262771    Centromere_region    10
chr2    113996917    113996927    chr2    46163086    169262771    Centromere_region    10

grep -c Centromere intersectBed_output
3
grep -c Telomere intersectBed_output
0

From this we can make Fisher's test:

>table = matrix(c(3,0,3-3,3-0), ncol=2, byrow=T)
>table
       [,1] [,2]
 [1,]    3    0
 [2,]    0    3
>fisher.test(table, alternative="greater")

Fisher's Exact Test for Count Data

   data:  table 
   p-value = 0.05
   alternative hypothesis: true odds ratio is greater than 1

But this seems way to complicated and probably not so accurate (it's possible to divide chromosome into bins and assign values).