BDgene

SNP Report

Basic Info
Name rs588409 dbSNP Ensembl
Location chr6:108237076 - 108237076(1)
Variant Alleles C/T
Ancestral Allele T
Minor Allele C
Minor Allele Frequence 0.175719
Functional Annotation intron_variant; NMD_transcript_variant.
Consequence to Transcript intron_variant(ENST00000230085, ENST00000349379, ENST00000368979, ENST00000426155); NMD_transcript_variant(ENST00000368979)
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
Kumar, R. A., 2008 A/G X2=1.55, OR (95% CI)=1.14 (0.92-1.43), P-value = ...... X2=1.55, OR (95% CI)=1.14 (0.92-1.43), P-value = 0.213 for bipolar disorder (I and II combined). X2=1.75, OR (95% CI)=1.16 (0.93-1.45), P-value = 0.186 for bipolar I disorder. X2=0.14, OR (95% CI)=1.11 (0.67-1.94), P-value = 0.707 for bipolar II disorder. More... Negative

SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
SNX3 sorting nexin 3 6q21 Mapped by Literature SNP
NR2E1 nuclear receptor subfamily 2, group E, member 1 6q21 1(1/0/0)

SNPs in LD with rs588409 (count: 3) View in gBrowse (chr6:108228848..108366620 )
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: 3)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Kumar, R. A., 2008 X2=0.78, OR (95% CI)=1.10 (0.88-1.43), P-value = 0.378 for SZ. No association was detected with schizophrenia. Negative

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