
SNP Report
Name | rs6265 dbSNP Ensembl | ||
---|---|---|---|
Location | 11:27658369 - 27658369(+) | ||
Variant Seq | T | ||
Ancestral Allele | C | ||
Ref Seq | C | ||
Minor Allele Frequence | 0.201278 | ||
Annotation | downstream_gene_variant; non_coding_transcript_exon_variant; missense_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | ||
Variant Effect | downstream_gene_variant(ENST00000532965); non_coding_transcript_exon_variant(ENST00000501176, ENST00000530686, ENST00000584049, ENST00000500662, ENST00000499568, ENST00000502161, ENST00000499008); missense_variant(ENST00000420794, ENST00000439476, ENST00000314915, ENST00000395986, ENST00000530861, ENST00000395983, ENST00000395981, ENST00000532997, ENST00000533131, ENST00000395980, ENST00000438929, ENST00000525528, ENST00000356660, ENST00000533246, ENST00000525950, ENST00000418212, ENST00000395978); 3_prime_UTR_variant(ENST00000530786); intron_variant(ENST00000530313); NMD_transcript_variant(ENST00000530786); non_coding_transcript_variant(ENST00000530313, ENST00000501176, ENST00000530686, ENST00000584049, ENST00000500662, ENST00000499568, ENST00000502161, ENST00000499008) | ||
SIFT Annotation | tolerated | ||
SIFT Variant Effect | tolerated(ENST00000420794, ENST00000439476, ENST00000314915, ENST00000395986, ENST00000530861, ENST00000395983, ENST00000395981, ENST00000532997, ENST00000533131, ENST00000395980, ENST00000438929, ENST00000525528, ENST00000356660, ENST00000533246, ENST00000525950, ENST00000418212, ENST00000395978) | ||
PolyPhen Annotation | probably_damaging; possibly_damaging | ||
PolyPhen Variant Effect | probably_damaging(ENST00000438929); possibly_damaging(ENST00000420794, ENST00000439476, ENST00000314915, ENST00000395986, ENST00000530861, ENST00000395983, ENST00000395981, ENST00000532997, ENST00000533131, ENST00000395980, ENST00000525528, ENST00000356660, ENST00000533246, ENST00000525950, ENST00000418212, ENST00000395978) | ||
rSNP? | Yes Link in rVarBase | ||
Related Regulatory Elements | n/a | ||
Chromatin State | Weak transcription;Strong transcription;Genic enhancers;Enhancers;ZNF genes & repeats | ||
No. of Marker's Association Results | 16 (Positive: 4; Negative: 12; Trend: 0) | ||
Source | Literature |
Reference | Phenotype | Statistical Values | Author Comments | Marker's Category |
---|---|---|---|---|
Bruenig, D.,2016 | CAPS score | In total sample: P-value=0.346, in the patient cohort: F(2)=...... In total sample: P-value=0.346, in the patient cohort: F(2)=0.501; P-value=0.607. More... | Te association between rs6265 (Val66Met) of BDNF gene and PT...... Te association between rs6265 (Val66Met) of BDNF gene and PTSD was not significant. More... | Non-significant |
Li, R. H.,2016 | Changes in PTSD severity between 6 and 12 months | P-value>0.05 P-value>0.05 | No significant differences were found between the scores at ...... No significant differences were found between the scores at 6 months and 12 months after the earthquake in the male subjects regardless of the genotypes. More... | Non-significant |
Li, R. H.,2016 | Changes in PTSD severity between 6 and 18 months | P-value>0.05 P-value>0.05 | No significant differences were found between the scores at ...... No significant differences were found between the scores at 6 months and 18 months after the earthquake in the male subjects regardless of the genotypes. More... | Non-significant |
Li, R. H.,2016 | Changes in PTSD severity between 12 and 18 months | P-value=0.034 P-value=0.034 | The scores at 18 months after the earthquake were significan...... The scores at 18 months after the earthquake were significantly lower when compared with those at 12 months after the earthquake only in the male Val/Val homozygote. More... | Significant |
van den Heuvel, L.,2016 | PTSD diagnosis | OR=0.261, P-value=0.276. OR=0.261, P-value=0.276. | BDNF Val66Met genotype was not significantly associated with...... BDNF Val66Met genotype was not significantly associated with the presence of PTSD. More... | Non-significant |
van den Heuvel, L.,2016 | CAPS score | U=656, P-value=0.264 U=656, P-value=0.264 | BDNF Val66Met genotype was not significantly associated with...... BDNF Val66Met genotype was not significantly associated with the severity of PTSD. More... | Non-significant |
Li, R. H.,2016 | PCL-C Scores of the Subjects with Different Genotypes of BDNF Val66Met at 6 or 12 or 18 Months After the Earthquake | The scores at 18 months after the earthquake compared with t...... The scores at 18 months after the earthquake compared with those at 12 months after the earthquake only in the male Val/Val homozygotes-23.00 (18.00-26.00) versus 24.00 (20.00-29.00), P-value=.034, but not in the male Met allele carriers. More... | There were no significant differences of the scores between ...... There were no significant differences of the scores between the subjects with the Val/Val genotype and the Met allele carriers at 6, 12, and 18 months after the earthquake regardless of gender. PCL-C scores were decreased in all subjects, female subjects but not male subjects when gender was taken into account, regardless of the genotypes at 12 months after the earthquake when compared with those at 6 months, and at 18 months when compared with those at 12 months or those at 6 months after the earthquake (Friedman M test). On the other hand, the scores at 18 months after the earthquake were significantly lower when compared with those at 12 months after the earthquake only in the male Val/Val homozygotes, but not in the male Met allele carriers. No significant differences were found between the scores at 6 months and 12 months and between the scores at 6 months and 18 months after the earthquake in the male subjects regardless of the genotypes. More... | Significant |
Dunn, E. C.,2014 | Post Traumatic Growth (PTG) | T4: joint test P-value> 0.05, variant P-value> 0.05. T4: joint test P-value> 0.05, variant P-value> 0.05. | We did not find any significant associations between the gen...... We did not find any significant associations between the genetic variants and PTG (P-values > 0.05). More... | Non-significant |
Dunn, E. C.,2014 | Post-traumatic stress symptoms (PTS) | T4: joint test P-value> 0.05, variant P-value> 0.05. T4: joint test P-value> 0.05, variant P-value> 0.05. | We did not find any significant associations between the gen...... We did not find any significant associations between the genetic variants and PTS (P-values > 0.05). More... | Non-significant |
Li, R. H.,2016 | Prevalence of PTSD in the Subjects with Different BDNF Val66Met Genotypes at 6 or 12 or 18 Months After the Earthquake | The article does not provide a specific chi-square test valu...... The article does not provide a specific chi-square test value. Potential Factors of Prevalence of PTSD in the Subjects with Different Genotypes of BDNF Val66Met: Gender was found to be the predictive factor of prevalence of PTSD in the Val/Val homozygotes at 12 months after the earthquake (OR?=?5.95, 95% CI?=?1.28-27.58, P-value=?.029). At 18 months, family member injury (OR?=?4.21, 95% CI?=?1.01-17.46, P-value=?.048) was the predictor of PTSD. In the Met allele carriers, the predictors of PTSD prevalence at 6 months after the earthquake were gender (OR?=?2.43, 95% CI?=?1.52-3.90, P-value.001), and previous trauma experience (OR?=?2.99, 95% CI?=?1.69-5.28, P-value.001). At 12 months, gender (OR?=?3.67, 95% CI?=?1.57-8.59, P-value=?.003) and previous trauma experience (OR?=?2.62, 95% CI?=?1.18-5.80, P-value=?.018) were also predictors of PTSD. Family member injury (OR?=?3.47, 95% CI?=?1.51-7.99, P-value=?.003) was an additional predictor at 12 months after the earthquake. At 18 months, age (OR?=?2.07, 95% CI?=?1.04-4.14, P-value=?.040), only child (OR?=?4.79, 95% CI?=?2.21-10.40, P-value.001), and exposure directly (OR?=?2.29, 95% CI?=?1.06-4.91, P-value=?.034) were the significant predictors of PTSD prevalence. More... | No significant differences of the prevalence were found betw...... No significant differences of the prevalence were found between the Val/Val homozygotes and the Met allele carriers at 6, 12, and 18 months after the earthquake regardless of gender. Significant decreases of PTSD prevalence were observed at 12 months and at 18 months after the earthquake when compared with that at 6 months after the earthquake regardless of gender and the genotype (chi-square test). More... | Significant |
Pivac, N.,2012 | Psychotic symptoms in PTSD | Case vs. control: genotype: X2= 2.426, P-value=...... Case vs. control: genotype: X2= 2.426, P-value= 0.297; allele: X2= 1.625, P-value= 0.202; Met carriers versus the homozygous Val/Val genotype: X2= 1.095, P-value= 0.295. Between mild, moderate and severe PTSD symptoms: genotype: X2= 5.532, P-value= 0.237; allele: X2= 1.00, P-value= 0.605; Met carriers versus the homozygous Val/Val genotype: X2= 1.356, P-value= 0.508. Veterans with PTSD comorbid with MDD and anxious depressive disorder vs. veterans with PTSD without any comorbidities: genotype: X2= 2.889, P-value= 0.236; allele: X2= 2.557, P-value= 0.110; Met carriers versus the homozygous Val/Val genotype: X2= 1.959, P-value= 0.162. Between veterans with PTSD with or without psychotic symptoms and veterans without PTSD: genotype: X2= 10.082, P-value= 0.039; allele: X2= 7.002, P-value= 0.030; Met carriers versus the homozygous Val/Val genotype: X2= 6.023, P-value= 0.049. More... | Rs6265 did not differ significantly when all veterans with P...... Rs6265 did not differ significantly when all veterans with PTSD were compared to veterans without PTSD. There were no significant differences in rs6265 between all veterans with PTSD with mild, moderate and severe PTSD symptoms. rs6265 did not differ significantly between all veterans with PTSD comorbid with MDD and anxious depressive disorder compared to veterans with PTSD without any comorbidities. Significant differences were detected in the frequencies of the BDNF Val66Met variants between veterans with PTSD with or without psychotic symptoms and veterans without PTSD. More... | Significant |
Zhang, H.,2006 | PTSD | Chi-square test Allele: P-value=0.233, Genotype: P-value=...... Chi-square test Allele: P-value=0.233, Genotype: P-value=0.306 More... | No evidence of association was found, inclusion of sex and a...... No evidence of association was found, inclusion of sex and age as factors in logistic regression analyses did not modify the absence of an association. More... | Non-significant |
Valente, N. L.,2011 | PTSD | Chi-square test. PTSD+, PTSD?, and community control groups...... Chi-square test. PTSD+, PTSD?, and community control groups: genotype: P-value= 0.65 More... | We did not find statistically significant difference son gen...... We did not find statistically significant difference son genotypic and allelic frequencies of the BDNF met/val polymorphism on PTSD+ and PTSD? groups and community control group. More... | Non-significant |
Wang, T.,2015 | PTSD | Our study did not found a significant overall effect of BDNF...... Our study did not found a significant overall effect of BDNF Val66Met on the susceptibility to PTSD under various genetic models. More... | Their pooled analyses did not demonstrate a significant over...... Their pooled analyses did not demonstrate a significant overall effect of the BDNF Val66Met allele on the development of PTSD within the selected genetic models. More... | Non-significant |
Lee, Heon-Jeong,2006 | PTSD | Genotype frequency: X2=0.43, df=2, P-value=0.81;...... Genotype frequency: X2=0.43, df=2, P-value=0.81; allele frequency: X2=0.32, df=1, P-value=0.57. More... | The BDNF Val66Met polymorphism had no signi?cant difference ...... The BDNF Val66Met polymorphism had no signi?cant difference between PTSD patients and controls in either the genotype or the allele frequency, although power was so limited. When this comparison was conducted separately by gender, there was no signi?cant difference between PTSD and controls. More... | Non-significant |
La Greca, A. M.,2013 | PTSD symptoms | Main effect of genotype on PTSD symptoms, P-value>0.05. Main effect of genotype on PTSD symptoms, P-value>0.05. | There was no main effect of genotype on PTSD symptoms. There was no main effect of genotype on PTSD symptoms. | Non-significant |
Reference | Phenotype | Environment | Statistical Values | Author Comments | Marker's Category |
---|---|---|---|---|---|
Dunn, E. C.,2014 | Post Traumatic Growth (PTG) | Hurricane exposure | T4: joint test P-value> 0.05, GxE interaction P-value> 0.05. T4: joint test P-value> 0.05, GxE interaction P-value> 0.05. | We did not find any significant associations between the gen...... We did not find any significant associations between the genetic variants and PTG (P-values > 0.05). More... | Non-significant |
Dunn, E. C.,2014 | Post-traumatic stress symptoms (PTS) | Hurricane exposure | Genetic variants and T3 or T4 PTS interaction: all P-values ...... Genetic variants and T3 or T4 PTS interaction: all P-values > 0.05. More... | We did not find any significant associations between the gen...... We did not find any significant associations between the genetic variants and T3 or T4 PTS (all P-values > 0.05). More... | Non-significant |
La Greca, A. M.,2013 | PTSD symptoms | Immediate loss and disruption, social support | GxExSS interaction:beta=-.27, P-value=.01 (emerged for the s...... GxExSS interaction:beta=-.27, P-value=.01 (emerged for the stressor of immediate loss/disruption). More... | When analyses were restricted to the youth who completed the...... When analyses were restricted to the youth who completed the social support measure, a significant GxExSS interaction emerged for the stressor of immediate loss/disruption; this interaction is depicted in Fig. 1. As expected, under the condition of low social support, there was a stronger association between stress levels and PTSD symptoms for youth with the met allele than for youth without the met allele. In contrast, under conditions of high support, youth with the met allele fared significantly better than youth without the met allele, especially among those reporting high levels of stress. More... | Significant |
La Greca, A. M.,2013 | PTSD symptoms | Ongoing loss and disruption | GxE interaction for ongoing loss and disruption: beta=.21, P...... GxE interaction for ongoing loss and disruption: beta=.21, P-value=.04; for the youth with the presence of the met allele: b=6.65, t(108)=3.34, P-value<.001; for youth without this allele: b=2.04, t(108)=1.84, non-significant. More... | For BDNF, and for the outcome of PTSD symptoms (Table 2), a ...... For BDNF, and for the outcome of PTSD symptoms (Table 2), a significant GxE interaction was obtained for ongoing loss and disruption. As expected, the association between ongoing loss and disruption and children's PTSD symptoms was stronger for the youth with the presence of the met allele than for youth without this allele. More... | Significant |
Approved Symbol | Approved Name | Location | No. of Association Results (Positive/Negative/Trend) ![]() |
---|---|---|---|
BDNF | brain-derived neurotrophic factor | 11p14.1 | 19(4/15/0) |
BDNF-AS | BDNF antisense RNA | 11p14.1 | Mapped by Literature SNP, Mapped by LD-proxy |
The LD data used here is based on 1000 Genome Phase I. LD SNP pairs were selected with a threshold r2<=0.8.
Literature-origin SNPs (count: 0)
LD-proxies (count: 41)

rs_ID | Literature-origin SNPs with LD | Annotation | r2[population] |
---|---|---|---|
rs16917204 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR] |
rs879048 | rs6265 | downstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8223[EUR] |
rs12417583 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8175[EUR] |
rs11030100 | rs6265 | non_coding_transcript_exon_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9046[ASN]; 0.8512[EUR]; 0.8033[AMR] |
rs2030323 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8454[ASN]; 0.8650[AMR] |
rs11030084 | rs6265 | intron_variant; non_coding_transcript_variant | 0.9356[EUR]; 0.9080[AMR] |
rs4923464 | rs6265 | downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9861[ASN]; 0.8819[EUR]; 0.8802[AMR] |
rs1488830 | rs6265 | downstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8223[EUR] |
rs2049045 | rs6265 | intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9676[EUR] |
rs7483762 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8367[EUR] |
rs10767664 | rs6265 | upstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8454[ASN]; 0.8650[AMR] |
rs12801337 | rs6265 | intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.8911[ASN]; 0.8650[AMR] |
rs4922793 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8454[ASN]; 0.8802[AMR] |
rs12790234 | rs6265 | intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.8911[ASN]; 0.8650[AMR] |
rs4923461 | rs6265 | upstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8367[EUR] |
rs7103411 | rs6265 | downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9791[ASN]; 0.8108[EUR]; 0.8502[AMR] |
rs10501087 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR] |
rs925947 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR] |
rs4074134 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8287[EUR] |
rs10767654 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8223[EUR] |
rs71480157 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8342[EUR] |
rs34379767 | rs6265 | downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.8911[ASN]; 0.8650[AMR] |
rs11030099 | rs6265 | non_coding_transcript_exon_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9046[ASN]; 0.8512[EUR]; 0.8033[AMR] |
rs4923466 | rs6265 | intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.8911[ASN]; 0.8650[AMR] |
rs4923457 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8287[EUR] |
rs4923460 | rs6265 | upstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8367[EUR] |
rs11030104 | rs6265 | downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 1.0000[ASN]; 0.8819[EUR]; 0.8802[AMR] |
rs12575096 | rs6265 | intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.8911[ASN]; 0.8959[AMR] |
rs16917237 | rs6265 | downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9722[ASN]; 0.8606[EUR]; 0.8802[AMR] |
rs1829469 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8454[ASN]; 0.8802[AMR] |
rs6484320 | rs6265 | downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9722[ASN]; 0.8108[EUR]; 0.8650[AMR] |
rs12807356 | rs6265 | downstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8911[ASN]; 0.8650[AMR] |
rs988748 | rs6265 | upstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8454[ASN]; 0.8218[AMR] |
rs4244531 | rs6265 | upstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8051[EUR] |
rs7926362 | rs6265 | intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.8911[ASN]; 0.8650[AMR] |
rs36029218 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8287[EUR] |
rs35038967 | rs6265 | downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant | 0.9722[ASN]; 0.8606[EUR]; 0.8802[AMR] |
rs35051342 | rs6265 | downstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8223[EUR]; 0.8131[AMR] |
rs4301747 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8367[EUR] |
rs4923463 | rs6265 | downstream_gene_variant; intron_variant; non_coding_transcript_variant | 0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR] |
rs12419948 | rs6265 | intron_variant; non_coding_transcript_variant | 0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR] |
Gene Symbol | Gene Existed in PTSDgene? | Tissue | Trans/Cis | Source |
---|---|---|---|---|
LRRC37A4P | No | Adipose Subcutaneous | cis | GTEx |
Copyright: Key Lab of Mental Health, Institute of Psychology, Chinese Academy of Sciences Feedback
Last update: April 1, 2018