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Post by plane83 on Sept 12, 2018 19:53:18 GMT
In the output of SMR using trans-eQTL, there are
trans_chr, trans_leftBound, trans_rightBound
and
topSNP,
What is the difference?
The eQTL SNP should be the one associated with GWAS signal and the gene expression, based on my understanding.
So, the two should be the same.
But in many cases, the two are different. topSNP and the trans_chr are not on the same chromosome.
Thanks,
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Post by futaozhang on Oct 6, 2018 22:41:16 GMT
In trans-eQTL SMR analysis, a specified window centered at a trans-eQTL will be tested as a trans-region.
trans_chr, trans_leftBound, trans_rightBound are the chromosome, the lower basepair position and the upper basepair position of this region respectively.
topSNP is the trans-eQTL which is selected as the instrument.
topSNP_chr is the same as trans_chr but might be different from ProbeChr.
And topSNP_bp must be between trans_leftBound and trans_rightBound.
Please have a double check with your result file.
A segment of the test result is attached below:
probeID ProbeChr Gene Probe_bp trans_chr trans_leftBound trans_rightBound topSNP topSNP_chr topSNP_bp A1 A2 Freq b_GWAS se_GWAS p_GWAS b_eQTL se_eQTL p_eQTL b_SMR se_SMR p_SMR p_HEIDI nsnp_HEIDI
cg01029838 7 NA 77428748 1 768448 2188032 rs3813199 1 1158277 A G 0.0941979 0.0081 0.0052 1.200000e-01 -0.545446 0.0523333 1.956703e-25 -0.0148502 0.00963938 1.234186e-01 1.671045e-01 10
The eQTL SNP should be the one associated with the exposure but not necessarily with the outcome.
Any questions please feel free to contact us here or by email.
Best wishes
Futao
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