BDgene

SNP Report

Basic Info
Name rs2596565 dbSNP Ensembl
Location chrCHR_HSCHR6_MHC_SSTO_CTG1:31379281 - 31379281(1)
Variant Alleles G/A
Minor Allele A
Minor Allele Frequence 0.0389377
Functional Annotation downstream_gene_variant; upstream_gene_variant.
Consequence to Transcript downstream_gene_variant(ENST00000424108); upstream_gene_variant(ENST00000425174, ENST00000449890, ENST00000417754, ENST00000433773, ENST00000440712, ENST00000423129, ENST00000419729, ENST00000427014, ENST00000416556)
No. of Studies 1 (Positive: 1; Negative: 0; 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
Andreassen OA, 2013 Conditional FDR; SCZ loci given BD: FDR=0.009 for SCZ and BD Conditional FDR; SCZ loci given BD: FDR=0.009 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

SNP related genes (count: 3)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
ZDHHC20P2 zinc finger, DHHC-type containing 20 pseudogene 2 6p21.3 Mapped by Literature SNP
HLA-S major histocompatibility complex, class I, S (pseudogene) 6p21.3 Mapped by Literature SNP
MICA MHC class I polypeptide-related sequence A 6p21.3 Mapped by LD-proxy


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Andreassen OA, 2013 Conditional FDR; SCZ loci given BD: P-value=0.00000933, FDR=0.077, FDR=0.009 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)