Metamoodics Gene Information

 

  Chromosome: chr17    Cytoband: q11.2    Gene: SLC6A4

 

MD - Genomewide Association Studies for SLC6A4


 

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Description

 
Shown here are the results for gene SLC6A4 from a mega-analysis of major depression carried out by the Psychiatric GWAS Consortium (PGC) of 9 GWAS studies. The total sample included 9,240 MDD cases and 9,519 controls all of European ancestry with data on ~1.2M genotyped and/or imputed SNPs.

 

Details of the methods for the mega-analysis are provided here.

 

 

Results Figure

 
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Figure Legend: A regional plot of association findings around the selected gene (+/-10Kb upstream and downstream of the union of the selected gene’s Refseq transcripts). The X-axis shows the position along the gene, the left Y-axis shows the -log10(p-value) and the right Y-axis shows the recombination rate estimated from HapMap data. Each point represents a SNP. The index SNP with the best p-value is depicted by a diamond, and the linkage disequilibrium of neighboring SNPs with the index SNP is color coded.

 

 

Results Table

 
CHR Marker pos_bp (hg18) A1 A2 INFO OR SE -LOG(10)P RSQUARE
17rs206671325575791AG0.96590.02190.9760.945770090136603(Index SNP)
17rs1215046525542469TC0.8511.0970.21510.6673595896125370.03796
17rs1696558125553268AG0.511.380.24780.6058986979599550.00501
17rs202093925574858AG0.9711.0240.27780.5562677585984030.45218
17rs990360225578212TG0.4252.6390.28470.5456125328530450.00501
17rs721499125596486AG0.9431.0220.34440.4629368572183830.16538
17rs148797125596879TC0.9470.9790.34560.4614262661931440.16538
17rs1696562825579551CG0.6021.0560.35230.4530873568187580.03395
17rs1165753625553368AG0.6231.080.35330.4518563625651540.03647
17rs14070125562658TC0.9651.0180.40630.3911531776735880.46427
17rs379480825555919TC0.9661.0160.4620.3353580244438740.44456
17rs807600525571336AG0.9640.98370.5520.2580609222708010.19806
17rs2552825574104TG0.970.98410.56180.2504182651344410.19806
17rs807166725576899TC0.971.0140.61380.2119731159041960.19044
17rs635425574024TG0.9730.98630.61580.2105603154328210.17594
17rs808102825547440AC0.9741.0330.62440.204537105609620.01016
17rs202093625574940AG0.9780.98670.62720.2025939503236180.19044
17rs190645125539605AG0.9780.99010.64540.1901710389321140.27213
17rs807396525583308TG0.4471.0330.680.1674910872937640.00982
17rs1782587725539314TC0.9731.0080.69480.1581401902249390.27782
17rs930362825551354TC0.9690.99170.69840.1558957693024870.31051
17rs381303425548930AC0.9760.99180.70380.1525507375008270.27213
17rs104217325549137AC0.9770.9920.71080.1482525808667360.27213
17rs2843745125592427AG0.351.0470.73650.132827248821350.0149
17rs722419925547852TG0.9751.0070.75120.1242444207419450.28423
17rs425141725575984TC0.8251.0030.94520.02447628703966860.10713
Table Legend: Table of association results for SNPs across the selected gene (+10Kb upstream and downstream of the
union of the selected gene’s Refseq transcripts).

 

 

References

 

Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium, Ripke S, Wray NR, Lewis CM, Hamilton SP, et al. A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry. 2013 Apr;18(4):497-511. doi: 10.1038/mp.2012.21. Epub 2012 Apr 3. PubMed PMID: 22472876.