BDgene

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)


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)