Dear Sir/Madam, I would like to download the unfiltered eQTL data (syn4622659) [SVA-adjusted]. The files in this directory are filtered by FDR and p-value. Thank You and With Regards, David

Created by davidgroenewoud
Great! I had not realized - since in the NRGR application a synapse code had to be included, I thought it was limited to only those data. Thanks!
Claudia- FYI, there is a single application for all the data. There is no separate access by Release.
Yes that helps, I will apply for Release 1 for now, thank you!
Claudia- We don't have unfiltered trans eQTLs to provide. Previous messages in this thread reference other sources for unfiltered cis eQTL. For CMC eQTL, you can find the adjusted expression used in the Fromer et al analysis here: https://www.synapse.org/#!Synapse:syn5607698. We adjusted for ancestry and Dx directly in the eQTL model. For that manuscript we used the 1000G imputation, you cited, however there is an HRC imputation available in Release 3. Hope that helps. Solly
Hi Solly, Thank you for your reply. Unfortunately the eQTL sets currently available will not work, because I am looking for unfiltered cis/trans eQTLs, so I will need to run it. It would be good to start with the same adjusted matrices that you have used for other analyses. Are the latest expression and imputed genotypes available the ones in Release 1? https://www.synapse.org/#!Synapse:syn5609488 https://www.synapse.org/#!Synapse:syn3275221 Thanks again, Claudia
Hi Claudia- Will the meta-analysis linked above work for you? We haven't generated eQTL on Release 3 yet. Solly
Hi Solly, I am also looking for the unfiltered eQTLs. Is it possible to link to the synapse code we would need to request to compute eQTL statistics in the same way as was computed by the consortium, so if possible the: 1) already adjusted expression matrices for gene and isoform. 2) imputed SNP data. For the latest release 3 (or if these are not available for the latest release, then for the previous)? Many thanks, Claudia
Hi David- We do not currently have unfiltered eQTL available. You may be interested in the eQTL available for the ROSMAP (syn16984409) and Mayo (syn16984411, syn16984410) cohorts through AMP-AD, as well as the meta-analysis, which contains ROSMAP, Mayo, CMC and HBCC (syn16984815). Solly

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