SNP Report

Basic Info

Name	rs1562313 dbSNP Ensembl
Location	chr2:100970993 - 100970993(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.236621
Functional Annotation	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000433012, ENST00000439150, ENST00000446644); non_coding_transcript_exon_variant(ENST00000474550); non_coding_transcript_variant(ENST00000474550); synonymous_variant(ENST00000335681, ENST00000448812); upstream_gene_variant(ENST00000450763, ENST00000471974)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Kripke, D. F.,2009	A/G		TDT: In BP: OR=1.261, CHISQ=4.957, P-value = 0.026, empirica...... TDT: In BP: OR=1.261, CHISQ=4.957, P-value = 0.026, empirical P-value = 0.0484, corrected empirical P-value = 0.9803 More...	Significant association was observed in the BP group. Significant association was observed in the BP group.	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
NPAS2	neuronal PAS domain protein 2	2q11.2	5(3/2/0)

SNPs in LD with rs1562313 (count: 2) View in gBrowse (chr2:100970993..100982215 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Literature-origin SNPs with LD	Functional Annotation	r²[population]
rs2278727		intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.899[CEU]
rs9679638		intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.894[CEU]

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

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