SNP Report

Basic Info

Name	rs231779 dbSNP Ensembl
Location	chr2:203869764 - 203869764(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.440296
Functional Annotation	intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000295854, ENST00000302823, ENST00000472206, ENST00000487393); non_coding_transcript_variant(ENST00000487393); upstream_gene_variant(ENST00000427473)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Liu, J,2011(a)	C/T		For BD: allele, OR[95%CI]=1.2599[1.1091-1.4311], P-value = 0...... For BD: allele, OR[95%CI]=1.2599[1.1091-1.4311], P-value = 0.0004, P-permutation=0.0008; genotype, P-value = 0.0018, P-permutation=0.0125 More...	Significant association was found . Significant association was found .	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
CTLA4	cytotoxic T-lymphocyte-associated protein 4	2q33	2(1/1/0)

SNPs in LD with rs231779 (count: 13) View in gBrowse (chr2:203829888..203876827 )

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]
rs231770	upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs11571315	upstream_gene_variant	1.0[CHB]; 0.974[CHD]; 1.0[JPT]
rs1427680	upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs231727	downstream_gene_variant	0.899[CHB]
rs736611	upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs11571292		1.0[CHB]; 0.974[CHD]; 1.0[JPT]
rs1024161		1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1427676	downstream_gene_variant	0.899[CHB]; 0.814[CHD]
rs926169		1.0[CHB]; 0.974[CHD]; 1.0[JPT]
rs3116513		0.841[CHB]; 0.947[JPT]
rs12992492		0.882[CHB]; 0.945[JPT]
rs231726	downstream_gene_variant	0.899[CHB]
rs231725	downstream_gene_variant	0.898[CHB]

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

Reference	Statistical Result	Description	Result Category
Liu, J,2011(a)	For SZ:allele, OR[95%CI]=1.2676[1.1135-1.4429], P-value = 0.0003, P-permutation=0.001;genotype, P-value = 0.0016, P-permutation=0.0145	Significant association was found .	Positive

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

Reference	Statistical Result	Description	Result Category
Liu, J,2011(a)	For MDD:allele, OR[95%CI]=1.2515[1.1015-1.4218], P-value = 0.0006, P-permutation=0.001;genotype, P-value = 0.0026, P-permutation=0.0201	Significant association was observed in MDD.	Positive