SNP Report

Basic Info

Name	rs2279574 dbSNP Ensembl
Location	chr12:89351700 - 89351700(1)
Variant Alleles	C/A
Ancestral Allele	C
Minor Allele	A
Minor Allele Frequence	0.466254
Functional Annotation	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000279488, ENST00000308385, ENST00000548755) SIFT Annotation: tolerated(ENST00000279488, ENST00000308385, ENST00000548755)
Consequence to Transcript	missense_variant(ENST00000279488, ENST00000308385, ENST00000548755); non_coding_transcript_exon_variant(ENST00000611513); non_coding_transcript_variant(ENST00000611513); upstream_gene_variant(ENST00000547140, ENST00000547291)
No. of Studies	3 (Positive: 3; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Lee, K. Y., 2006 (a)	T/G	allelic P-value = 0.027, genotypic P-value = 0.062 for total...... allelic P-value = 0.027, genotypic P-value = 0.062 for total patients; allelic P-value = 0.691, genotypic P-value = 0.52 for male patients; allelic P-value = 0.008, genotypic P-value = 0.02 for female patients with bipolar disorder More...	G allele was significantly more common in bipolar patients t...... G allele was significantly more common in bipolar patients than controls. G allele frequency was also significantly increased in female bipolar patients compared to female controls , but there was no group difference in males. When allele and genotype distribution were compared between the bipolar and schizophrenia groups, no significant difference was found. However, G allele was observed more commonly in bipolar females than their schizophrenic counterparts. More...	Positive
Yosifova, A.,2009	A/C	Allelic association: 1st screening: P-value = 0.0041, 2nd sc...... Allelic association: 1st screening: P-value = 0.0041, 2nd screening: P-value = 0.43, total: P-value = 0.026 More...	Significant association was observed in 1st screening and to...... Significant association was observed in 1st screening and total sample. More...	Positive
Kim, S. H., 2012 (a)	T/G	chi-square P-value = 0.0813, Permutation P-value = 0.2472, X...... chi-square P-value = 0.0813, Permutation P-value = 0.2472, X²=3.0382, OR=1.21; chi-square P-value = 0.015, Permutation P-value = 0.0469, X²=5.9218, OR=1.442 for female subjects, chi-square P-value = 0.9545, Permutation P-value = 1, X²=0.0033, OR=0.9909 for male subjects More...	showed nominally significant allelic associations with BD, b...... showed nominally significant allelic associations with BD, but not with SPR, in female patients More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
DUSP6	dual specificity phosphatase 6	12q22-q23	5(3/2/0)

SNPs in LD with rs2279574 (count: 13) View in gBrowse (chr12:89332250..89394010 )

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: 13)

rs_ID	Functional Annotation	r²[population]
rs1427828	non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 0.977[TSI]; 1.0[CHB]; 0.951[CHD]; 0.953[JPT]
rs797266		0.893[CHB]; 0.815[JPT]
rs770082		0.88[CEU]; 0.828[TSI]; 0.945[CHB]; 0.861[CHD]; 0.857[JPT]
rs12819667	downstream_gene_variant; upstream_gene_variant	1.0[CEU]; 0.944[CHB]; 0.909[JPT]
rs7305095		0.893[CHB]; 0.815[JPT]
rs770083		0.88[CEU]; 0.954[TSI]; 0.945[CHB]; 0.861[CHD]; 0.861[JPT]
rs11105273		0.834[CHB]; 0.818[JPT]
rs10506971	upstream_gene_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 0.951[CHD]; 0.953[JPT]
rs1427829	upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 0.953[JPT]
rs704067		0.956[CEU]; 0.834[CHB]; 0.909[JPT]
rs10506965		0.869[CEU]; 0.838[CHB]; 0.806[JPT]
rs704061		1.0[CEU]; 0.978[TSI]; 0.945[CHB]; 0.859[CHD]; 0.909[JPT]
rs7135819		0.893[CHB]; 0.806[JPT]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Kim, S. H., 2012 (a)	chi-square P-value = 0.9205, Permutation P-value = 0.9992, X²=0.01, OR=1.012; chi-square P-value = 0.8087, Permutation P-value = 1, X²=0.0586, OR=1.047 for female subjects, chi-square P-value = 0.7677, Permutation P-value = 0.93, X²=0.0872, OR=0.954 for male subjects	showed nominally significant allelic associations with BD, but not with SPR, in female patients	Negative
Lee, K. Y., 2006 (a)	allelic P-value = 0.911, genotypic P-value = 0.991 for total patients; allelic P-value = 0.95, genotypic P-value = 0.865 for male patients; allelic P-value = 0.776, genotypic P-value = 0.95 for female patients with schizophrenia	G allele was not different between schizophrenic patients and controls. When allele and genotype distribution were compared between the bipolar and schizophrenia groups, no significant difference was found. However, G allele was observed more commonly in bipolar females than their schizophrenic counterparts.	Negative

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