SNP Report

Basic Info

Name	rs16840252 dbSNP Ensembl
Location	chr2:203866796 - 203866796(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.127596
Functional Annotation	upstream_gene_variant.
Consequence to Transcript	upstream_gene_variant(ENST00000295854, ENST00000302823, ENST00000427473, ENST00000472206, ENST00000487393)
No. of Studies	1 (Positive: 0; Negative: 1; 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]=0.8429[0.7098-1.0009], P-value = 0...... For BD: allele, OR[95%CI]=0.8429[0.7098-1.0009], P-value = 0.051, P-permutation=0.3067; genotype, P-value = 0.0742, P-permutation=0.415 More...	No significant association was observed. No significant association was observed.	Negative

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 rs16840252 (count: 15) View in gBrowse (chr2:203854006..203926214 )

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]
rs13414502		0.888[CHB]; 0.846[JPT]
rs859839		0.888[CHB]; 0.846[JPT]
rs6714468		0.888[CHB]; 0.846[JPT]
rs7597297		0.877[CHB]; 0.846[JPT]
rs11904099		0.888[CHB]; 0.846[JPT]
rs6414164		0.888[CHB]; 0.823[JPT]
rs6752680		0.888[CHB]; 0.846[JPT]
rs13421616		0.888[CHB]; 0.826[CHD]; 0.846[JPT]
rs10197010	downstream_gene_variant	0.846[JPT]
rs231755		0.888[CHB]; 0.846[JPT]
rs2162610		0.888[CHB]; 0.846[JPT]
rs231757		0.888[CHB]; 0.846[JPT]
rs4553808	upstream_gene_variant	0.821[CHB]
rs11890284		0.888[CHB]; 0.846[JPT]
rs231731		0.888[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]=0.7931[0.6680-0.9417], P-value = 0.0081, P-permutation=0.0665;genotype, P-value = 0.0117, P-permutation=0.0935	Significant association was found, but the significance was lost after permutation.	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]=0.9253[0.7769-1.1021], P-value = 0.3841, P-permutation=0.9537;genotype, P-value = 0.3011, P-permutation=0.8963	No significant association was observed.	Negative