BDgene

SNP Report

Basic Info
Name rs2252865 dbSNP Ensembl
Location chr1:8362616 - 8362616(1)
Variant Alleles T/C
Ancestral Allele C
Minor Allele T
Minor Allele Frequence 0.201877
Functional Annotation downstream_gene_variant; intron_variant.
Consequence to Transcript downstream_gene_variant(ENST00000460659, ENST00000464367, ENST00000465125, ENST00000488215, ENST00000492766); intron_variant(ENST00000337907, ENST00000377464, ENST00000400907, ENST00000400908, ENST00000476556, ENST00000505225)
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 T/C Conditional FDR; SCZ loci given BD: FDR=0.03 for SCZ and BD,...... Conditional FDR; SCZ loci given BD: FDR=0.03 for SCZ and BD, ||Conditional FDR; BD loci given SCZ: P-value=0.000219, FDR=0.44657, FDR=0.01306 for BD and SCZ||Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.03 for BD and SZ, Z-score=3.696 for BD More... 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<0.05. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.05 with schizophrenia and bipolar disorder considered jointly. More... Positive

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
RERE arginine-glutamic acid dipeptide (RE) repeats 1p36.23 Mapped by Literature SNP

SNPs in LD with rs2252865 (count: 0) View in gBrowse (chr1:8362616..8362616 )

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=0.000476, FDR=0.377, FDR=0.03 for SCZ and BD||Conditional FDR; BD loci given SCZ: FDR=0.01306 for BD and SCZ||Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.03 for BD and SZ, Z-score=3.494 for SZ 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<0.05. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.05 with schizophrenia and bipolar disorder considered jointly. Positive

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