SNP Report

Basic Info

Name	rs6746896 dbSNP Ensembl
Location	chr2:96745212 - 96745212(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.214257
No. of Studies	5 (Positive: 3; Negative: 0; Trend: 2)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 5)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Sklar, P.,2011	A/G		Primary GWAS P-value(GC)=0.00000233, OR=1.14; replication P-...... Primary GWAS P-value(GC)=0.00000233, OR=1.14; replication P-value(1-sided)=0.0386, OR=1.05; Combined GWAS and replication P-value(GC)=0.00000236, OR=1.1 More...	Suggestive association was found. Suggestive association was found.	Trend
Lim C.H., 2014	A/G	G	All ethnicities: OR=1.36, 95%CI =1.08-1.71, P-value=0.009; M...... All ethnicities: OR=1.36, 95%CI =1.08-1.71, P-value=0.009; Malay: OR=1.09, 95%CI =0.74-1.60, P-value=0.678; Chinese: OR=1.63, 95%CI =1.14-2.34, P-value=0.007; Indian: OR=1.21, 95%CI =0.73-2.00, P-value=0.471 More...	rs6746896 shows significant differences in allelic distribut...... rs6746896 shows significant differences in allelic distribution between both BPD and SZ patients and controls for the pooled subjects (P =0.009 and 0.001, respectively). More...	Positive
Byrne, E. M., 2014			P-value=2.45E-09 P-value=2.45E-09	The gene CNNM4 on chromosome 2 is located downstream of the ...... The gene CNNM4 on chromosome 2 is located downstream of the genome-wide significant SNP (rs6746896, BPD P=2.45*10-9) and ranks second among the extended circadian gene list for association with BPD. More...	Positive
Chen, D. T.,2011		A	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 = 3.57E-08, Random effects P-value = 4.19E-07, I²=52.07, Q test=6.26, Q test P-value = 0.1; European and Asian-ancestry phase I & phase II samples: Fixed effects P-value = 1.59E-08, Random effects P-value = 1.78E-07, I²=57.92, Q test=11.88, Q test P-value = 0.036; European-ancestry phase I samples: Fixed effects P-value = 1.66E-09, Random effects P-value = 2.62E-08, I²=0, Q test=0.55, Q test P-value = 0.761; European-ancestry phase I and phase II samples: Fixed effects P-value = 1.35E-09, Random effects P-value = 3.23E-08, I²=43.88, Q test=7.13, Q test P-value = 0.129 More...	The results suggest novel association findings. The results suggest novel association findings.	Positive
Green, E. K.,2012	A/G		BD ImmunoChip:P-value = 0.011,OR = 1.146;ImmunoChip, PGC-BD ...... BD ImmunoChip:P-value = 0.011,OR = 1.146;ImmunoChip, PGC-BD combined data:P-balue = 0.000000114,OR = 1.106 More...	Suggestive association was found. Suggestive association was found.	Trend

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
LMAN2L	lectin, mannose-binding 2-like	2q11.1	2(2/0/0)
CNNM4	cyclin and CBS domain divalent metal cation transport mediator 4	2q11.2	1(1/0/0)

SNPs in LD with rs6746896 (count: 1) View in gBrowse (chr2:96745212..96747751 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 1)

rs_ID	Literature-origin SNPs with LD	Functional Annotation	r²[population]
rs2314398			0.867[CEU]

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

Reference	Statistical Result	Description	Result Category
Lim C.H., 2014	All ethnicities: OR=1.34, 95%CI =1.12-1.61, P-value=0.001; Malay: OR=1.50, 95%CI =1.07-2.10, P-value=0.020; Chinese: OR=1.21, 95%CI =0.94-1.55, P-value=0.148; Indian: OR=1.59, 95%CI =0.98-2.58, P-value=0.061	rs6746896 shows significant differences in allelic distribution between both BPD and SZ patients and controls for the pooled subjects (P =0.009 and 0.001, respectively).	Positive

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