Hi,

I have been using CNVannotator to annotate my CNV regions and worked pretty well for me. I can retrieve a lot features from there. Only thing is for my CNV regions I found CpG sites but these sites are not annotated to corresponding gene names. I just receive the regions that match and retrieve CpG information, now I want to know to which gene these regions correspond to that got a hit in their database. I found an online tool lynx where you can provide regions in order of

chr8:12595527-43811979
chr8:183585-7808664
chr8:12595527-43926760
chr14:69961223-70005628

And then I can retrieve gene names for these regions. I would like to know if this is a right approach to annotate the CpG regions that I get for my CNV regions. The regions of CNV that matches with CpG regions in CNVannotator are returned as below. I am now taking the regions of Matched position to know the gene names of these CpG sites with Lynx. I would like some suggestions. I do not have strand information so I cannot use Ensemble or Homer. Any inputs are appreciated

                                                        # of       # of     Percentage     Percentage      Ratio of
Query position              Matched position            CpG in     G/C      of island      of island       observed to
                                                        island              that is CpG    that is G/C     expected CpG
chr10:6130750-6131499       chr10:6130786-6131774       102        618      20.6           62.6            1.06
chr10:70883500-70884249     chr10:70883663-70884353     78         465      22.6           67.4            1
chr10:75910500-75911249     chr10:75910836-75911480     50         435      15.5           67.5            0.71
chr11:17410000-17757749     chr11:17756056-17758286     226        1405     20.3           63              1.02
chr11:63530500-67829499     chr11:63529888-63531834     171        1271     17.6           65.3            0.8