I have the hadoop configured with 

<property> 
  <name>dfs.data.dir</name> 
  <value>/mnt/hadoop/data</value> 
  <description>Default block replication. 
  The actual number of replications can be specified when the file is
created. 
  The default is used if replication is not specified in create time. 
  </description> 
</property> 


and my HBase has 

<property> 
    <name>hbase.rootdir</name> 
    <value>hdfs://cdh1:54310/hbase</value> 
    <description>The directory shared by region servers. 
    </description> 
  </property> 

the hdfs://cdh1:54310 is the hadoop url. 

I would have expected the hbase dir , created at /mnt/hadoop/data/hbase but
it is being created at the user root. When I run MR on hadoop independent of
HBase , the data files are created at /mnt/hadoop/data/ thus proving that
hadoop independently is honoring the dfs.data.dir. 

NOTE that I have the hdfs-site.xml sym linked up in  [HBase_Dir]/conf though
I do not think it matters.
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