SNP Report

Basic Info

Name	rs2271893 dbSNP Ensembl
Location	chr2:96739703 - 96739703(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.154952
Functional Annotation	intron_variant; NMD_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000264963, ENST00000377079, ENST00000434524, ENST00000434865, ENST00000440610, ENST00000446780, ENST00000449221); NMD_transcript_variant(ENST00000434524, ENST00000434865, ENST00000440610, ENST00000446780, ENST00000449221)
No. of Studies	3 (Positive: 2; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Chen, D. T.,2011		G	Meta-analysis results by ancestry: European and Asian-ancest...... Meta-analysis results by ancestry: European and Asian-ancestry phase I samples: Fixed effects P-value = 1.08E-08, Random effects P-value = 5.20EC10, I²=43.83, Q test=5.34, Q test P-value = 0.148; European and Asian-ancestry phase I & phase II samples: Fixed effects P-value = 5.21E-09, Random effects P-value = 2.20EC10, I²=52.31, Q test=10.49, Q test P-value = 0.063; European-ancestry phase I samples: Fixed effects P-value = 1.21E-09, Random effects P-value = 1.73EC10, I²=16.16, Q test=2.39, Q test P-value = 0.303; European-ancestry phase I and phase II samples: Fixed effects P-value = 9.81EC10, Random effects P-value = 1.34EC10, I²=51.27, Q test=8.21, Q test P-value = 0.084 More...	The results suggest novel association findings. The results suggest novel association findings.	Positive
Lim C.H., 2014	G/A	A	All ethnicities: OR=1.12, 95%CI =0.85-1.48, P-value=0.429; M...... All ethnicities: OR=1.12, 95%CI =0.85-1.48, P-value=0.429; Malay: OR=0.83, 95%CI =0.49-1.41, P-value=0.490; Chinese: OR=1.15, 95%CI =0.77-1.71, P-value=0.495; Indian: OR=1.31, 95%CI =0.73-2.30, P-value=0.363 More...	No significant association was observed. No significant association was observed.	Negative
Andreassen OA, 2013			Conditional FDR; BD loci given SCZ: P-value=0.0000185, FDR=0...... Conditional FDR; BD loci given SCZ: P-value=0.0000185, FDR=0.18928, FDR=0.0096 for BD and SCZ More...	This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
LMAN2L	lectin, mannose-binding 2-like	2q11.1	2(2/0/0)

SNPs in LD with rs2271893 (count: 0) View in gBrowse (chr2:96739703..96739703 )

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

Reference	Statistical Result	Description	Result Category
Lim C.H., 2014	All ethnicities: OR=1.24, 95%CI =0.99-1.56, P-value=0.060; Malay: OR=2.63, 95%CI =1.40-4.97, P-value=0.003; Chinese: OR=0.86, 95%CI =0.64-1.15, P-value=0.297; Indian: OR=2.76, 95%CI =1.46-5.20, P-value=0.002	rs2271893 C allele frequency was significantly higher in SZ patients compared with healthy controls, a condition observed in Malays and Indians (P= 0.002 and P= 0.003, respectively).	Positive
Andreassen OA, 2013	Conditional FDR; BD loci given SCZ: FDR=0.0096 for BD and SCZ	This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'.	Positive

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