SNP Report

Basic Info

Name	rs1978340 dbSNP Ensembl
Location	chr2:170813611 - 170813611(1)
Variant Alleles	G/A
Ancestral Allele	A
Minor Allele	A
Minor Allele Frequence	0.232029
Functional Annotation	downstream_gene_variant; intron_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000418106, ENST00000451730, ENST00000455988); intron_variant(ENST00000454603); upstream_gene_variant(ENST00000344257, ENST00000358196, ENST00000375272, ENST00000414527, ENST00000429023, ENST00000445006, ENST00000455008, ENST00000456864, ENST00000493875, ENST00000625689)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Yosifova, A.,2009	A/G		Allelic association: P-value = 0.62 Allelic association: P-value = 0.62	No significant association was observed No significant association was observed	Negative
Lundorf, M. D.,2005	C/T		Fisher's exact test: for BPAD, in Danish sample set, P-value...... Fisher's exact test: for BPAD, in Danish sample set, P-value(allele)=0.028, P-value(genotype)=0.062; in Scottish sample set, P-value(allele)=0.87, P-value(genotype)=0.98 More...	Significant associations were found in Danish sample set, bu...... Significant associations were found in Danish sample set, but not in Scottish sample set. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
GAD1	glutamate decarboxylase 1 (brain, 67kDa)	2q31	2(1/1/0)

SNPs in LD with rs1978340 (count: 11) View in gBrowse (chr2:170774121..170815681 )

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]
rs10930440	downstream_gene_variant; upstream_gene_variant	0.814[CEU]
rs4668315	downstream_gene_variant; upstream_gene_variant	0.848[CEU]
rs2287111	intron_variant	0.902[TSI]
rs34137349		0.9[TSI]
rs3791878	downstream_gene_variant; intron_variant; upstream_gene_variant	0.902[TSI]
rs2287110	intron_variant	0.902[TSI]
rs7568115	intron_variant	0.901[TSI]
rs7600585	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.902[TSI]
rs17694708	downstream_gene_variant; upstream_gene_variant	0.801[CEU]
rs1420378	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.814[CEU]; 0.902[TSI]
rs2883888		0.9[TSI]

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Lundorf, M. D.,2005	Fisher's exact test:for SZ, in Scottish sample set, P-value(allele)=0.57, P-value(genotype)=0.74	No significant association was observed.	Negative

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