BDgene

SNP Report

Basic Info
Name rs11191580 dbSNP Ensembl
Location chr10:103146454 - 103146454(1)
Variant Alleles T/C
Ancestral Allele T
Minor Allele C
Minor Allele Frequence 0.146965
Functional Annotation intron_variant; NMD_transcript_variant; non_coding_transcript_variant.
Consequence to Transcript intron_variant(ENST00000343289, ENST00000369857, ENST00000404739, ENST00000452156, ENST00000461461, ENST00000470299); NMD_transcript_variant(ENST00000452156, ENST00000461461); non_coding_transcript_variant(ENST00000369857)
No. of Studies 3 (Positive: 3; Negative: 0; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? NO

SNP related studies (count: 3)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Hamshere, M. L.,2012 T/C Association analysis: P-value = 0.018 Association analysis: P-value = 0.018 Significant association was observed in BD. Significant association was observed in BD. Positive
Andreassen OA, 2013 Conditional FDR; SCZ loci given BD: FDR=0.005 for SCZ and BD Conditional FDR; SCZ loci given BD: FDR=0.005 for SCZ and BD To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. More... Positive
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013 T/C Association analysis:P-value = 0.0000000111 when five disord...... Association analysis:P-value = 0.0000000111 when five disorders were combined. More... Significant association was observed in cross-disorder analy...... Significant association was observed in cross-disorder analysis. More... Positive

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
NT5C2 5'-nucleotidase, cytosolic II 10q24.32 2(2/0/0)

SNPs in LD with rs11191580 (count: 33) View in gBrowse (chr10:102947259..103179458 )
The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r2<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 33)


Overlap with SZ from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Hamshere, M. L.,2012 Association analysis:OR=1.19, P-value = 0.01 Significant association was observed in SZ. Positive association was observed in SZ.
Andreassen OA, 2013 Conditional FDR; SCZ loci given BD: P-value=0.00000171, FDR=0.049, FDR=0.005 for SCZ and BD To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.32. Positive

Overlap with MDD from cross-disorder studies (count: 0)

Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback Acknowledgements
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Last update: March 31, 2016