I am not sure what eQTL data is used in the "SMR Vlues Janson" result (" Final_SMR_TWAS_Jansen_Validation.tsv" at https://www.synapse.org/#!Synapse:syn22076063). Is it the "eQTLmateAnalisis" result("Cortex_MetaAnalysis_ROSMAP_CMC_HBCC_Mayo_cis_eQTL_release.csv" at https://www.synapse.org/#!Synapse:syn16984815) or other sigle eQTL results(such as "DLPFC_ROSMAP_cis_eQTL_release.csv" at https://www.synapse.org/#!Synapse:syn16984409)? Here is another question. In an eQTL result data, which column is the "effect/reference allel", "A1" or "A2"? Thanks.

Created by CaoLuolong
thanks? I know Jansen's meta-GWAS data is used in SMR analysis, i.e. the "SMR Vlues Janson" result (" Final_SMR_TWAS_Jansen_Validation.tsv" at https://www.synapse.org/#!Synapse:syn22076063). But I do not konw which one ** eQTL data** is used in above-mentioned SMR analysis (among below 4 eQTL files)? 1)https://www.synapse.org/#!Synapse:syn16984815 2)https://www.synapse.org/#!Synapse:syn16984411 3)https://www.synapse.org/#!Synapse:syn16984409 4)https://www.synapse.org/#!Synapse:syn16984410
Hi @CaoLuolong Jansen eqtl data was derived from: Jansen IE, Savage JE, Watanabe K, Bryois J, Williams DM, Steinberg S, et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer?s disease risk. Nat Genet. 2019 Mar;51(3):404?13. Files are available here: https://ctg.cncr.nl/software/summary_statistics Data is coded per [cnsgenomics SMR](https://cnsgenomics.com/software/smr/#SMR) input requirements: _Important: ?A1? needs to be the effect allele with ?A2? being the other allele and ?freq? needs to be the frequency of ?A1?._ https://cnsgenomics.com/software/smr/#SMR

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