Try this site Sarah. 

http://webspace.qmul.ac.uk/rlowe/marmalaid/

Ovine adipose NR3C1

Highlighted black tracks. Note strong UMR in the promoter,

 The methylation status of genes differs between cell types and tissues. Additionally it is influenced by age, gender and other factors. NR3C1 's methylation pattern has shown to be susceptible to early life stress events as well. Contrary to what has been often observed in cancer studies, the NR3C1  gene is not either methylated (high levels) or not (low levels), but rather 'small' changes in methylation levels. So there is not 1 overall answer summarising the methylation status of the NR3C1 gene. So do you have a particular tissue/cell type in mind, do you have own data? You can visualise those in e.g. UCSC browser. If you want to browse through existing data and get an idea I can recommand the http://www.roadmapepigenomics.org/data/ 

Thank you very much indeed Dr. Ross L Tellam but i need it in humans

Thanks a lot Dr. Fleur, i know, but what do you mean by "'small' changes in methylation levels" ! Yes i work on buccal epithelial cells. Yes i managed to use the UCSC and reached this: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr5%3A143277931-143435512&hgsid=500008221_ZcznwQBRbdyaljemEOaGpTweQDv4

But can't spot the quantitative methylation status of the gene

With small changes I mean changes in methylation status 10% or less than 10%.

The UCSC browser allows you to view the CG density and CpG islands as welll. As for your data, the UCSC browser indicates where the reads map, but what you are looking at really depends what you uploaded. Did you use bisulfate sequencing? or others and which analysis steps were already performed?

If you'd like to compare with data from others I suggest this roadmap epigenomics consortium. http://www.roadmapepigenomics.org/  

Thank you very much indeed Dr. Fleur for your help and valuable replies. I didn't upload anything because i don't want to analyze the methylation of the DNA i have, rather i want to know the overall/average methylation status of the NR3C1 Gene in human saliva "epithelial cells" to make statistical work based on this quantitative data.

Hi Sarah,

NR3C1 is a very large gene. Most of it will be hypermethylated and a few regulatory regions will be hypomethylated. Hence on average I think that the complete gene will have a mean beta value approaching 1.0. This number will not be very informative from a statistical point of view.

Are you using a DNA methylation array (where each probe only reports a small region of the gene) or whole genome methylation data (which will report all CpG within the gene)? If the former then you need to know where in the gene the probe is located. Buccal cell methylation patterns have been published and these may be the best source of the information you require.

Cheers

Ross

Thanks a lot Dr. Ross. Yes i focus specifically on the CpG sites 1–29 in exon 1F promoter in the gene. Is it hypomethylated? Can i find its info in this UCSC database: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr5%3A143277931-143435512&hgsid=500008221_ZcznwQBRbdyaljemEOaGpTweQDv4

Hi Sarah,

If your focus of interest is only the exon 1F of NR3C1 gene in humans I would say it is mostly hypomethylated in healthy tissue (with methylation percentages usually below 5%).

You can freely access a research paper by Yehuda and colleagues at Research Gate (https://www.researchgate.net/publication/260232875_Lower_Methylation_of_Glucocorticoid_Receptor_Gene_Promoter_1F_in_Peripheral_Blood_of_Veterans_with_Posttraumatic_Stress_Disorder) where CpG-specific methylation percentages at exon 1F are detailed for their sample (n = 122). 

Of course, and as Ms. Leenen already pointed out, this percentage will depend as a function of gender, age, the cell type of  interest, presence of early stress and psychopathology, among other factors.

As a matter of fact, whenever your CpG sites of interest are located within a CpG island, they will be most certainly hypomethylated.

I hope this helps,

Helena

Article Lower Methylation of Glucocorticoid Receptor Gene Promoter 1...

OMG!!! WOW you're Dr. Helena Palma-Gudiel ! I'm fond of your work and studies. I'm extremely lucky to be talking to you. Thanks a lot for your informative reply.

Have a look at a couple of the papers on my page as well, we have done a number of studies on the 1F promoter.............

A good paper to start with would be Cao-Lei et al J. Psych Res 2013