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.

rs_ID	Functional Annotation	r²[population]
rs10457177	intron_variant; NMD_transcript_variant	0.824[CEU]
rs487467	intron_variant; NMD_transcript_variant	1.0[CEU]; 0.914[TSI]
rs632817	upstream_gene_variant	0.824[CEU]; 0.816[TSI]

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)