BDgene

SNP Report

Basic Info
Name rs886424 dbSNP Ensembl
Location chrCHR_HSCHR6_MHC_SSTO_CTG1:30806442 - 30806442(1)
Variant Alleles C/T
Ancestral Allele C
Minor Allele T
Minor Allele Frequence 0.0405351
Functional Annotation intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant.
Consequence to Transcript intron_variant(ENST00000419357); non_coding_transcript_exon_variant(ENST00000399196); non_coding_transcript_variant(ENST00000399196, ENST00000419357, ENST00000419202, ENST00000452623, ENST00000419202, ENST00000452623, ENST00000415307, ENST00000324858, ENST00000324858, ENST00000415307, ENST00000430758, ENST00000431091, ENST00000430758, ENST00000431091, ENST00000438637, ENST00000400508, ENST00000400508, ENST00000438637, ENST00000432546, ENST00000427874, ENST00000427874, ENST00000432546)
No. of Studies 1 (Positive: 0; Negative: 1; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? NO

SNP related studies (count: 1)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Bergen, S. E.,2012 T logistic regression: P-value > E-05 logistic regression: P-value > E-05 No significant association was observed in BD. No significant association was observed in BD. Negative

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
LINC00243 long intergenic non-protein coding RNA 243 6p21.33 Mapped by Literature SNP

SNPs in LD with rs886424 (count: 68) View in gBrowse (chrCHR_HSCHR6_MHC_SSTO_CTG1:30627966..31002078 )
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: 68)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Bergen, S. E.,2012 logistic regression:for SZ new sample, OR=0.71, P-value = 8.80E-06, for SZ full sample, OR=0.68, P-value = 4.54E-08 Significant association was observed in SZ. 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