SNP Report

Basic Info

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

SNP related association results

Normal genetic study related association results (count: 16)

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 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

G*E study related association result (count: 4)

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

SNP related genes (count: 2)

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

SNPs in LD with rs6265 (count: 41)

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]
rs4923460	rs6265	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8367[EUR]
rs35051342	rs6265	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8223[EUR]; 0.8131[AMR]
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]
rs925947	rs6265	intron_variant; non_coding_transcript_variant	0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR]
rs4923466	rs6265	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8911[ASN]; 0.8650[AMR]
rs7483762	rs6265	intron_variant; non_coding_transcript_variant	0.8367[EUR]
rs4244531	rs6265	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8051[EUR]
rs10767654	rs6265	intron_variant; non_coding_transcript_variant	0.8223[EUR]
rs12801337	rs6265	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8911[ASN]; 0.8650[AMR]
rs34379767	rs6265	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8911[ASN]; 0.8650[AMR]
rs12417583	rs6265	intron_variant; non_coding_transcript_variant	0.8175[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]
rs11030084	rs6265	intron_variant; non_coding_transcript_variant	0.9356[EUR]; 0.9080[AMR]
rs16917237	rs6265	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9722[ASN]; 0.8606[EUR]; 0.8802[AMR]
rs12790234	rs6265	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8911[ASN]; 0.8650[AMR]
rs4301747	rs6265	intron_variant; non_coding_transcript_variant	0.8367[EUR]
rs71480157	rs6265	intron_variant; non_coding_transcript_variant	0.8342[EUR]
rs4923463	rs6265	downstream_gene_variant; 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]
rs6484320	rs6265	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9722[ASN]; 0.8108[EUR]; 0.8650[AMR]
rs16917204	rs6265	intron_variant; non_coding_transcript_variant	0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR]
rs4923457	rs6265	intron_variant; non_coding_transcript_variant	0.8287[EUR]
rs10767664	rs6265	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8454[ASN]; 0.8650[AMR]
rs2049045	rs6265	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9676[EUR]
rs1488830	rs6265	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8223[EUR]
rs1829469	rs6265	intron_variant; non_coding_transcript_variant	0.8454[ASN]; 0.8802[AMR]
rs4923461	rs6265	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8367[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]
rs12575096	rs6265	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8911[ASN]; 0.8959[AMR]
rs35038967	rs6265	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9722[ASN]; 0.8606[EUR]; 0.8802[AMR]
rs4922793	rs6265	intron_variant; non_coding_transcript_variant	0.8454[ASN]; 0.8802[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]
rs2030323	rs6265	intron_variant; non_coding_transcript_variant	0.8454[ASN]; 0.8650[AMR]
rs12419948	rs6265	intron_variant; non_coding_transcript_variant	0.8914[ASN]; 0.8526[EUR]; 0.8316[AMR]
rs36029218	rs6265	intron_variant; non_coding_transcript_variant	0.8287[EUR]
rs12807356	rs6265	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8911[ASN]; 0.8650[AMR]
rs7926362	rs6265	intron_variant; NMD_transcript_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]
rs4074134	rs6265	intron_variant; non_coding_transcript_variant	0.8287[EUR]
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]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
LRRC37A4P	No	Adipose Subcutaneous	cis	GTEx