SNP Report

Basic Info

Name	rs770087 dbSNP Ensembl
Location	chr12:89350996 - 89350996(1)
Variant Alleles	A/C
Ancestral Allele	C
Minor Allele	C
Minor Allele Frequence	0.217452
Functional Annotation	downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000279488, ENST00000547291) SIFT Annotation: tolerated(ENST00000279488, ENST00000547291)
Consequence to Transcript	downstream_gene_variant(ENST00000548755); intron_variant(ENST00000308385); missense_variant(ENST00000279488, ENST00000547291); non_coding_transcript_exon_variant(ENST00000547140); non_coding_transcript_variant(ENST00000547140); upstream_gene_variant(ENST00000611513)
No. of Studies	1 (Positive: 1; Negative: 0; 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
Kim, S. H., 2012 (a)	T/G		chi-square P-value = 0.006, Permutation P-value = 0.0227, X<...... chi-square P-value = 0.006, Permutation P-value = 0.0227, X²=7.5649, OR=2.219; chi-square P-value = 0.0007, Permutation P-value = 0.0015, X²=11.3843, OR=4.162 for female subjects, chi-square P-value = 0.9623, Permutation P-value = 1, X²=0.0022, OR=1.021 for male subjects More...	showed nominally significant association with BD, and the em...... showed nominally significant association with BD, and the empirical P-value with 10, 000 permutations for each SNP was also significant. 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 rs770087 (count: 14) View in gBrowse (chr12:89348954..89384460 )

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]
rs704084		1.0[CHD]
rs1472212		1.0[CHB]
rs704080	downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]
rs1650342		1.0[CHB]
rs1689437	upstream_gene_variant	1.0[CHB]; 1.0[CHD]
rs1688549		1.0[CHB]
rs1689408		1.0[CHB]; 1.0[CHD]
rs1689406		1.0[CHB]
rs1631726	upstream_gene_variant	1.0[CHB]
rs765646	downstream_gene_variant; upstream_gene_variant	1.0[CHB]
rs704083	non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]
rs704074	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs1689410	downstream_gene_variant; upstream_gene_variant	1.0[CHB]
rs1689411	downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]

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

Reference	Statistical Result	Description	Result Category
Kim, S. H., 2012 (a)	chi-square P-value = 0.9919, Permutation P-value = 1, X²=0.0001, OR=0.9961; chi-square P-value = 0.4652, Permutation P-value = 0.8983, X²=0.5333, OR=1.559 for female subjects, chi-square P-value = 0.4958, Permutation P-value = 0.9196, X²=0.464, OR=0.7172 for male subjects	showed nominally significant allelic associations with BD, but not with SPR, in female patients	Negative

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