BDgene

SNP Report

Basic Info
Name rs6265 dbSNP Ensembl
Location chr11:27658369 - 27658369(1)
Variant Alleles C/T
Ancestral Allele C
Minor Allele T
Minor Allele Frequence 0.201278
Functional Annotation 3_prime_UTR_variant; downstream_gene_variant; intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant.
Polyphen Annotation: possibly damaging(ENST00000314915, ENST00000356660, ENST00000395978, ENST00000395980, ENST00000395981, ENST00000395983, ENST00000395986, ENST00000418212, ENST00000420794, ENST00000439476, ENST00000525528, ENST00000525950, ENST00000530861, ENST00000532997, ENST00000533131, ENST00000533246); probably damaging(ENST00000438929)
SIFT Annotation: tolerated(ENST00000314915, ENST00000356660, ENST00000395978, ENST00000395980, ENST00000395981, ENST00000395983, ENST00000395986, ENST00000418212, ENST00000420794, ENST00000439476, ENST00000525528, ENST00000525950, ENST00000530861, ENST00000532997, ENST00000533131, ENST00000533246, ENST00000438929)
Consequence to Transcript 3_prime_UTR_variant(ENST00000530786); downstream_gene_variant(ENST00000532965); intron_variant(ENST00000530313); missense_variant(ENST00000314915, ENST00000356660, ENST00000395978, ENST00000395980, ENST00000395981, ENST00000395983, ENST00000395986, ENST00000418212, ENST00000420794, ENST00000439476, ENST00000525528, ENST00000525950, ENST00000530861, ENST00000532997, ENST00000533131, ENST00000533246, ENST00000438929); NMD_transcript_variant(ENST00000530786); non_coding_transcript_exon_variant(ENST00000499008, ENST00000499568, ENST00000500662, ENST00000501176, ENST00000502161, ENST00000530686, ENST00000584049); non_coding_transcript_variant(ENST00000499008, ENST00000499568, ENST00000500662, ENST00000501176, ENST00000502161, ENST00000530313, ENST00000530686, ENST00000584049)
No. of Studies 17 (Positive: 7; Negative: 10; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? YES

SNP related studies (count: 17)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Ivanova, M. A.,2012 Val66Met Case–control study:C(Val) allele:80.72%/75.95%(case/contro...... Case–control study:C(Val) allele:80.72%/75.95%(case/control); P=0.093; genotype Met/Met:3.07%/6.96%(case/control) for the narrow phenotype. More... No significant association was observed. No significant association was observed. Negative
Neves-Pereira, M.,2005 G/A allele: X2=0.377, P-value = 0.54; genotype: P-val...... allele: X2=0.377, P-value = 0.54; genotype: P-value > 0.05 More... No significant associations were found in BD. No significant associations were found in BD. Negative
Kim, B., 2008 differences in allele (X2 = 0.400, P- value= 0.82...... differences in allele (X2 = 0.400, P- value= 0.821) and genotype (X2= 0.220, P- value = 0.640) More... Allelic distributions did not differ significantly between b...... Allelic distributions did not differ significantly between bipolar patients and controls. More... Negative
Yosifova, A.,2009 C/T Allelic association: 1st screening: P-value = 0.0079, 2nd sc...... Allelic association: 1st screening: P-value = 0.0079, 2nd screening: P-value = 0.14, total: P-value = 0.0033 More... Significant association was observed in 1st screening and to...... Significant association was observed in 1st screening and total sample. More... Positive
Xu, J., 2010 Val66Met Val genotype test: P-value = 0.00884 for all patients, P-value =...... genotype test: P-value = 0.00884 for all patients, P-value = 0.0391 for BD-I patients, P-value = 0.0364 for BD-II patients. Allele test: P-value = 0.425 for all patients, P-value = 0.903 for BD-I patients, P-value = 0.0516 for BD-II patients. The odds ratio for patients with Met/Met was 1.44 (95% CI=1.070-1.950; P=0.016), for those with bipolar I disorder 1.335 (95% CI=0.973-1.832; P=0.146) and for those with bipolar II disorder 2.07 (95% CI=1.242-3.454; P=0.011), respectively. More... the Met allele rather than the Val allele increased the risk...... the Met allele rather than the Val allele increased the risk for BPD in our Han population. More... Positive
Kanazawa, T., 2007 Val(G)/Met(A) Met P-value = 0.161, OR=0.95 (95% CI: 0.88-1.02), z=1.40, hetero...... P-value = 0.161, OR=0.95 (95% CI: 0.88-1.02), z=1.40, heterogeneity P-value = 0.769, X2=6.53 (d.f.=10) for bipolar disorder More... The data showed stronger evidence for association but still ...... The data showed stronger evidence for association but still did not attain significance. No evidence of heterogeneity was observed among these studies More... Negative
Gonzalez-Castro, T. B., 2014 Meta-analysis: Val allele: with heterogeneity: random effect...... Meta-analysis: Val allele: with heterogeneity: random effects: OR=1.06, 95%CI=0.95-1.18, P-value=0.31; without heterogeneity: random effects: OR=1.02; 95%CI=0.97-1.08; P-value=0.38. Met allele: with heterogeneity: random effects: OR=0.93, 95%CI=0.84-1.04, P-value=0.31; without heterogeneity: random effects: OR=0.97, 95%CI=0.92-1.03, P-value=0.38. Caucasian: with heterogeneity: random effects: OR=1.11, 95%CI=0.90-1.38, P-value=0.59; without heterogeneity: random effects: OR=1.03, 95%CI=0.94-1.12, P-value=0.91. Asian: without heterogeneity: random effects: OR=0.99, 95%CI=0.92-1.06, P-value=0.21. Additive model: with heterogeneity: random effects: OR=1.06, 95%CI=0.91-1.23, P-value=0.49; without heterogeneity: random effects: OR=1.01, 95%CI=0.89-1.14, P-value=0.73. Dominant model: with heterogeneity: random effects: OR=1.07, 95%CI=0.93-1.22, P-value=0.23; without heterogeneity: random effects: OR=1.05, 95%CI=0.93-1.18, P-value=0.54. Recessive model: with heterogeneity: random effects: OR=1.02, 95%CI=0.93-1.12, P-value=0.46; without heterogeneity: random effects: OR=1.04, 95%CI=0.96-1.13, P-value=0.15. Case-control study: BDNF Val66Met genotype groups: P-value=0.84; Allele groups: P-value=0.55, OR=0.87, 95%CI=0.56-1.35 More... No significant associations were observed in all models and ...... No significant associations were observed in all models and subgroups. More... Negative
Seifuddin, F.,2012 C/T Meta-analysis OR=0.93, 95% CI=0.87-1.00, P-value = 0.050 Meta-analysis OR=0.93, 95% CI=0.87-1.00, P-value = 0.050 No significance was found after correction for multiple test...... No significance was found after correction for multiple testing. More... Negative
Liu, L., 2008 Average PDT statistic P-value = 0.4 for the model 1; averag...... Average PDT statistic P-value = 0.4 for the model 1; average PDT statistic P-value = 0.26 for the model 2; average PDT statistic P-value = 0.06 for the model 3 between the SNP and bipolar disorder. More... The previously reported Val66Met polymorphism (rs6265) was n...... The previously reported Val66Met polymorphism (rs6265) was not significantly associated with either bipolar disorder or rapid cycling More... Negative
Oswald, P., 2004 G>A X2 (df=2)=2.0, P-value = 0.37 for genotypes; X X2 (df=2)=2.0, P-value = 0.37 for genotypes; X2 (df=1)=0.00, P-value = 0.94 for alleles distributions More... No significant differences were found in the frequency of ge...... No significant differences were found in the frequency of genotypes and alleles between controls and BPAD patients More... Negative
Lohoff, F. W.,2005(c) Val/Met Val chi-square test: genotype P-value = 0.062, allele P-value = ...... chi-square test: genotype P-value = 0.062, allele P-value = 0.028 More... Significant associations were found in allele frequencies . Significant associations were found in allele frequencies . Positive
Sears, C.,2011 A FBAT: MAF=0.173, P-value = 0.04 FBAT: MAF=0.173, P-value = 0.04 Significant association was found . Significant association was found . Positive
Hosang, G. M.,2010 Val66Met Met X2 test: Genotypic distribution, X2=15...... X2 test: Genotypic distribution, X2=15.65, df=2, P-value = 0.001 More... Significant association was found in BD. Significant association was found in BD. Positive
Kremeyer, B., 2006 A/G P-value = 0.001, X2=10.77, df=1 P-value = 0.001, X2=10.77, df=1 At the Val66Met polymorphism there is a significant over-tra...... At the Val66Met polymorphism there is a significant over-transmission of the Val allele. More... Positive
Wang, Z.,2012 Val66Met Met genotype: X2 = 6.18, df = 2, P =0.046; allele: X...... genotype: X2 = 6.18, df = 2, P =0.046; allele: X2 = 5.01, df = 1, P-value = 0.025 More... Val66Met is associated with BD Val66Met is associated with BD Positive
Schumacher, J.,2005 G/A Armitage Trend Test: in Bonn sample, for BPAD, P-value(odds ...... Armitage Trend Test: in Bonn sample, for BPAD, P-value(odds ratio)=0.924(1.01) More... No significant association was observed. No significant association was observed. Negative
Neves, F. S.,2011 T/C chi-square test: allele, P-value = 0.474, OR(95%CI)=0.83(0.5...... chi-square test: allele, P-value = 0.474, OR(95%CI)=0.83(0.50-1.37), genotype, P-value = 0.123 More... No significant association was observed. No significant association was observed. Negative

SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
BDNF brain-derived neurotrophic factor 11p14.1 37(24/12/1)
BDNF-AS BDNF antisense RNA 11p14.1 Mapped by Literature SNP

SNPs in LD with rs6265 (count: 17) View in gBrowse (chr11:27520076..27728178 )
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: 17)


Overlap with SZ from cross-disorder studies (count: 3)
Reference Statistical Result Description Result Category
Neves-Pereira, M.,2005 allele:X2=7.89, P-value = 0.0049, OR=1.48, upper 95%CI=1.95, lower CI=1.13;genotype:X2=10.1; P-value = 0.0015; OR=1.68; upper 95% CI=1.22, lower 95% CI=2.32. Significant association was observed in SZ. Positive
Kanazawa, T., 2007 P-value = 0.944, OR=1.00 (95% CI: 0.89-1.11), z=0.07, heterogeneity P-value = 0.078, X2=19.47 (d.f.=12) for schizophrenia The meta-analysis of data showed no support for an association with the putative risk allele (Met). Some evidence of heterogeneity was observed among the studies, but this did not attain statistical significance. Negative
Schumacher, J.,2005 Armitage Trend Test:in Bonn sample, for Schizophrenia, P-value(odds ratio)=0.093(1.17) No significant association was observed. Negative

Overlap with MDD from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Schumacher, J.,2005 Armitage Trend Test:in Bonn sample, for MDD, P-value(odds ratio)=0.314(1.10);in Munich sample, for MDD, P-value(odds ratio)=0.881(1.02) No association was observed. Negative

Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback Acknowledgements
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Last update: March 31, 2016