SNP Report

Basic Info

Name	rs231777 dbSNP Ensembl
Location	chr2:203868865 - 203868865(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	T
Minor Allele Frequence	0.135184
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]=0.815[0.6859-0.9683], P-value = 0....... For BD: allele, OR[95%CI]=0.815[0.6859-0.9683], P-value = 0.0199, P-permutation=0.142; genotype, P-value = 0.0588, P-permutation=0.3416 More...	Significant association was found, but the significance was ...... Significant association was found, but the significance was lost after permutation. More...	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 rs231777 (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]
rs6714468		0.888[CHB]; 1.0[JPT]
rs10197010	downstream_gene_variant	0.846[JPT]
rs4553808	upstream_gene_variant	0.821[CHB]; 1.0[JPT]
rs231757		0.888[CHB]; 0.935[CHD]; 1.0[JPT]
rs2162610		0.888[CHB]; 0.935[CHD]; 1.0[JPT]
rs231755		0.888[CHB]; 1.0[JPT]
rs859839		0.888[CHB]; 1.0[JPT]
rs6752680		0.888[CHB]; 0.825[CHD]; 1.0[JPT]
rs11904099		0.888[CHB]; 0.935[CHD]; 1.0[JPT]
rs231731		0.888[CHB]; 0.847[JPT]
rs13421616		0.888[CHB]; 1.0[CHD]; 1.0[JPT]
rs6414164		0.888[CHB]; 0.825[CHD]; 1.0[JPT]
rs13414502		0.888[CHB]; 1.0[JPT]
rs7597297		0.877[CHB]; 1.0[JPT]
rs11890284		1.0[CHB]; 0.825[CHD]; 1.0[JPT]

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]=0.813[0.6827-0.9683], P-value = 0.0201, P-permutation=0.1559;genotype, P-value = 0.0631, P-permutation=0.3912	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]=0.8736[0.7334-1.0405], P-value = 0.1295, P-permutation=0.5924;genotype, P-value = 0.2679, P-permutation=0.8568	No significant association was observed.	Negative