SNP Report

Basic Info

Name	rs9470080 dbSNP Ensembl
Location	6:35678658 - 35678658(+)
Variant Seq	C
Ancestral Allele	T
Ref Seq	T
Minor Allele Frequence	0.363419
Annotation	intron_variant
Variant Effect	intron_variant(ENST00000542713, ENST00000539068, ENST00000357266, ENST00000536438)
SIFT Annotation	deleterious; tolerated
SIFT Variant Effect	deleterious(ENST00000542713); tolerated(ENST00000539068, ENST00000357266, ENST00000536438)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000539068, ENST00000542713, ENST00000357266, ENST00000536438)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	Enhancers;Weak transcription;Strong transcription;Genic enhancers
No. of Marker's Association Results	16 (Positive: 7; Negative: 9; 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
Watkins, L. E.,2016	Lifetime PTSD symptoms	Main smaple: F=6.33, P-value=0.002. Replication sample: F=7....... Main smaple: F=6.33, P-value=0.002. Replication sample: F=7.36, P-value=0.001. More...	Main effect of this SNP is significant. Main effect of this SNP is significant.	Significant
Watkins, L. E.,2016	Re-experiencing symptoms	F=5.49, P-value=0.004 F=5.49, P-value=0.004	Main effect of this SNP is not significant. Main effect of this SNP is not significant.	Non-significant
Watkins, L. E.,2016	Avoidance symptoms (DSM-IV)	F=6.02, P-value=0.003 F=6.02, P-value=0.003	Main effect of this SNP is significant. Main effect of this SNP is significant.	Significant
Watkins, L. E.,2016	Emotional numbing	F=2.13, P-value=0.12 F=2.13, P-value=0.12	Main effect of this SNP is not significant. Main effect of this SNP is not significant.	Non-significant
Watkins, L. E.,2016	Hyperarousal symptoms	F=6.34, P-value=0.002 F=6.34, P-value=0.002	Main effect of this SNP is significant. Main effect of this SNP is significant.	Significant
Watkins, L. E.,2016	Intrusion symptoms	F=4.74, P-value=0.009 F=4.74, P-value=0.009	Main effect of this SNP is not significant. Main effect of this SNP is not significant.	Non-significant
Watkins, L. E.,2016	Avoidance symptoms (DSM-5)	F=3.00, P-value=0.051 F=3.00, P-value=0.051	Main effect of this SNP is not significant. Main effect of this SNP is not significant.	Non-significant
Watkins, L. E.,2016	Negative alterations in cognitions and mood symptoms	F=4.46, P-value=0.012 F=4.46, P-value=0.012	Main effect of this SNP is not significant. Main effect of this SNP is not significant.	Non-significant
Watkins, L. E.,2016	Alterations in arousal and reactivity symptoms	F=14.01, P-value<0.001 F=14.01, P-value<0.001	Main effect of this SNP is significant. Main effect of this SNP is significant.	Significant
David, A. C.,2012	Improvement in CAPS PTSD symptoms scores	Linear regression: B=8.05, SE(B)=5.1, beta=0.38, P-value>0....... Linear regression: B=8.05, SE(B)=5.1, beta=0.38, P-value>0.05, R²=0.34. More...	A significant association of this SNP with improvement in PT...... A significant association of this SNP with improvement in PTSD symptom scores. Similar results were found when peritraumatic distress was used as a predictor instead of peritraumatic dissociation. More...	Non-significant
Xie, P.,2010	Lifetime PTSD	In African American, main effect: OR=0.58, 95%CI=0.41-0.82,...... In African American, main effect: OR=0.58, 95%CI=0.41-0.82, P-value=0.0025. In European American, it showed no significant association between genotypes and PTSD (data not shown). More...	In the primary analyses, logistic GEE regression showed no s...... In the primary analyses, logistic GEE regression showed no significant association betweenFKBP5?genotypes and PTSD in AAs or EAs (data not shown). When main FKBP5 genotype effects and their interaction effects with childhood adversity were entered into the logistic regression models simultaneously, all four SNPs were significantly associated with the development of PTSD in AAs. After correction for multiple testing, it remained significant (Bonferroni correction, threshold P-value=0.05/4=0.0125). SNP rs9470080 had the strongest conditional effect. However, in EAs, none of the four SNPs were associated with the development of PTSD when the interactive effect of genotype and childhood adversity was also in the logistic regression model.The results from the secondary analyses are very similar to the primary results. More...	Significant
David, A. C.,2012	Memory Performance	Relation between FKBP5 gene and memory performance at T2: r...... Relation between FKBP5 gene and memory performance at T2: r=0.02, P-value=0.94. More...	FKBP5 alone was not found to be associated with memory perfo...... FKBP5 alone was not found to be associated with memory performance at T2. More...	Non-significant
Dunn, E. C.,2014	Post Traumatic Growth (PTG)	T4: joint test P-value> 0.05, variant P-value=0.024. T4: joint test P-value> 0.05, variant P-value=0.024.	We found a significant association between FKBP5 and PTG. We found a significant association between FKBP5 and PTG.	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
David, A. C.,2012	PTSD Diagnostic Status at T2	(remitted vs. unremitting PTSD) recessive alleles were combi...... (remitted vs. unremitting PTSD) recessive alleles were combined and genotype frequencies were compared using the following model: CT+TT vs. CC, T allele, X²=6.77, P-value=0.004. More...	These results suggest that the CC genotype at rs9470080 is a...... These results suggest that the CC genotype at rs9470080 is associated with unremitting chronic PTSD. More...	Significant
Binder, E. B.,2008	PTSD Symptoms (PSS scores)	No available detail information. No available detail information.	We found no significant main effect of FKBP5 genotypes on PS...... We found no significant main effect of FKBP5 genotypes on PSS total score. More...	Non-significant

G*E study related association result (count: 16)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Watkins, L. E.,2016	Lifetime PTSD symptoms	Childhood abuse	Main smaple: F=3.65, P-value=0.006. Replication sample: F=6....... Main smaple: F=3.65, P-value=0.006. Replication sample: F=6.09, P-value=0.002. More...	The interaction effect of the SNP and childhood abuse is sig...... The interaction effect of the SNP and childhood abuse is significant. More...	Significant
Watkins, L. E.,2016	Re-experiencing symptoms	Childhood abuse	F=1.23, P-value=0.29 F=1.23, P-value=0.29	The interaction effect of the SNP and childhood abuse is not...... The interaction effect of the SNP and childhood abuse is not significant. More...	Non-significant
Watkins, L. E.,2016	Avoidance symptoms (DSM-IV)	Childhood abuse	F=0.62, P-value=0.54 F=0.62, P-value=0.54	The interaction effect of the SNP and childhood abuse is not...... The interaction effect of the SNP and childhood abuse is not significant. More...	Non-significant
Watkins, L. E.,2016	Emotional numbing	Childhood abuse	F=0.29, P-value=0.75 F=0.29, P-value=0.75	The interaction effect of the SNP and childhood abuse is not...... The interaction effect of the SNP and childhood abuse is not significant. More...	Non-significant
Watkins, L. E.,2016	Hyperarousal symptoms	Childhood abuse	F=5.14, P-value=0.006 F=5.14, P-value=0.006	The interaction effect of the SNP and childhood abuse is not...... The interaction effect of the SNP and childhood abuse is not significant. More...	Non-significant
Watkins, L. E.,2016	Intrusion symptoms	Childhood abuse	F=4.74, P-value=0.009 F=4.74, P-value=0.009	The interaction effect of the SNP and childhood abuse is not...... The interaction effect of the SNP and childhood abuse is not significant. More...	Non-significant
Watkins, L. E.,2016	Avoidance symptoms (DSM-5)	Childhood abuse	F=3.00, P-value=0.051 F=3.00, P-value=0.051	The interaction effect of the SNP and childhood abuse is not...... The interaction effect of the SNP and childhood abuse is not significant. More...	Non-significant
Watkins, L. E.,2016	Negative alterations in cognitions and mood symptoms	Childhood abuse	F=4.46, P-value=0.012 F=4.46, P-value=0.012	The interaction effect of the SNP and childhood abuse is not...... The interaction effect of the SNP and childhood abuse is not significant. More...	Non-significant
Watkins, L. E.,2016	Alterations in arousal and reactivity symptoms	Childhood abuse	F=14.01, P-value<0.001 F=14.01, P-value<0.001	The interaction effect of the SNP and childhood abuse is sig...... The interaction effect of the SNP and childhood abuse is significant. More...	Significant
Xie, P.,2010	Lifetime PTSD	Childhood adversity (Three types of childhood adversity were considered in this study: namely, witnessing or experiencing a violent crime, experiencing sexual abuse, and experiencing physical abuse.)	In African Americans, the effects of childhood adversity x F...... In African Americans, the effects of childhood adversity x FKBP5 genotype on risk for PTSD (before correction for multiple tests): OR=1.96, CI=1.24-3.10, P-value=0.0040. More...	Before correction for multiple tests, two of the four SNPs i...... Before correction for multiple tests, two of the four SNPs in FKBP5 significantly modified the effect of childhood adversity on risk for PTSD in AAs (rs9296158: OR=1.69, 95% CI=1.05-2.71, P=0.03; rs9470080: OR=1.96, 95% CI=1.24-3.10, P=0.004). (These same two SNPs also were the most significant in the previous study by Binder et al, (2008).) After Bonferroni correction, the signal from rs9470080 remained significant. There was no interactive effect of FKBP5 genotypes and childhood adversity in EAs. The results from the secondary analyses are very similar to the primary results. More...	Significant
David, A. C.,2012	Memory Performance	Peritraumatic Responses (PDEQ, peritraumatic dissociation)	Association between the new GxE interaction variable and mem...... Association between the new GxE interaction variable and memory performance at T2 with partial correlations controlling for main effects: r=0.52, P-value=0.03. Post-hoc analyses (bivariate correlations) were conducted, the dominant homozygous genotypes CC: r=-0.68, P-value=0.03; other genotypes: r=0.04, P-value=0.91. More...	Significant partial correlations were found between the new ...... Significant partial correlations were found between the new G x PDEQ (i.e., peritraumatic dissociation) variable and memory performance for this SNP. These results suggest an interactive effect of FKBP5 SNPs and subjective trauma severity on memory performance. Significant negative correlations were found for individuals with the dominant homozygous genotypes. No significant correlations were found for the other genotypes. More...	Significant
David, A. C.,2012	Memory Performance	Peritraumatic Responses (PDI, peritraumatic distress)	Association between the new GxE interaction variable and mem...... Association between the new GxE interaction variable and memory performance at T2 with partial correlations controlling for main effects: r=0.50, P-value=0.04. Post-hoc analyses (bivariate correlations) were conducted, the dominant homozygous genotypes CC: r=-0.69, P-value=0.03; other genotypes: r=0.30, P-value=0.40. More...	Significant partial correlations were found between the new ...... Significant partial correlations were found between the new G x PDI (i.e., peritraumatic distress) variable and memory performance for this SNP. These results suggest an interactive effect of FKBP5 SNPs and subjective trauma severity on memory performance. Significant negative correlations were found for individuals with the dominant homozygous genotypes. No significant correlations were found for the other genotypes. More...	Significant
Binder, E. B.,2008	Pearson correlation R value of CTQ Total Score and PSS Scores	Child abuse	CC vs TT group: Z values for difference of correlation coeff...... CC vs TT group: Z values for difference of correlation coefficient=1.9;CT vs CC group: Z values for difference of correlation coefficient=1.20;TT vs CT group: Z values for difference of correlation coefficient=1.03. More...	They observed non-significantly higher correlations of CTQ t...... They observed non-significantly higher correlations of CTQ total score and PSS score between some genotype group of this SNP. More...	Non-significant
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
Binder, E. B.,2008	PTSD Symptoms (PSS scores)	Child abuse	Interaction of it with child abuse level (to predict PTSD sy...... Interaction of it with child abuse level (to predict PTSD symptoms),an interaction P-value<.002 (after correcting for multiple tesing). After adjusting for variables (controlling for BDI score as a continuous measure of depression symptoms or the 4-level non-child abuse trauma variable in addtion to age and sex) , the interaction P-value=0.06. More...	We identified the SNP that showed significant interactions w...... We identified the SNP that showed significant interactions with child abuse afterc orrecting for multiple testing. More...	Significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
FKBP5	FK506 binding protein 5	6p21.31	25(12/13/0)
MIR5690	microRNA 5690	6	Mapped by LD-proxy, rSNP target

SNPs in LD with rs9470080 (count: 36)

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: 3)

rs_ID	Annotation	No. of Association Results(Positive/Negative/Trend)	r²[population]

rs9296158	intron_variant(ENST00000539068, ENST00000542713, ENST00000536438, ENST00000357266)	17(9/8/0)	0.8463[EUR]; 0.8352[AMR]
rs1360780	intron_variant(ENST00000542713, ENST00000357266, ENST00000539068, ENST00000536438)	21(8/13/0)	0.8576[EUR]
rs4713916	upstream_gene_variant(ENST00000411131); intron_variant(ENST00000536438)	1(0/1/0)	0.8064[EUR]

LD-proxies (count: 33)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs12153967	rs9470080 rs4713916	downstream_gene_variant; intron_variant	0.8017[EUR]
rs9357201	rs1360780 rs9296158 rs9470080	upstream_gene_variant; intron_variant	0.9576[EUR]; 0.8494[AFR]; 0.8134[AMR]
rs943297	rs9470080 rs4713916	downstream_gene_variant; intron_variant	0.8233[EUR]
rs6902321	rs9470080	upstream_gene_variant; intron_variant	0.8721[EUR]
rs7759392	rs9470080 rs4713916	intron_variant	0.8748[EUR]
rs6902124	rs1360780 rs9296158 rs9470080 rs3800373	intron_variant	0.8576[EUR]
rs2395635	rs9470080 rs4713916	upstream_gene_variant; intron_variant	0.8121[EUR]
rs4713903	rs9470080	upstream_gene_variant; intron_variant	0.9161[EUR]
rs9357202	rs1360780 rs9296158 rs9470080	upstream_gene_variant; intron_variant	0.9637[EUR]; 0.8272[AFR]; 0.8142[AMR]
rs9296159	rs1360780 rs9296158 rs9470080	downstream_gene_variant; intron_variant	0.9524[EUR]; 0.8575[AFR]; 0.8049[AMR]
rs3798347	rs1360780 rs9296158 rs9470080 rs3800373	intron_variant	0.8576[EUR]; 0.8128[AMR]
rs6912833	rs9470080	upstream_gene_variant; intron_variant	0.8929[EUR]
rs3800372	rs1360780 rs9296158 rs9470080	intron_variant	0.9878[EUR]; 0.9754[AFR]; 0.9756[AMR]
rs4713904	rs9470080	intron_variant	0.9098[EUR]
rs6931118	rs1360780 rs9296158 rs9470080	downstream_gene_variant; intron_variant	0.9758[EUR]; 0.8597[AFR]; 0.8466[AMR]
rs9368885	rs1360780 rs9296158 rs9470080	upstream_gene_variant; intron_variant	0.9878[EUR]; 0.9122[AFR]; 0.9515[AMR]
rs9368878	rs1360780 rs9296158 rs9470080 rs3800373	intron_variant	0.8576[EUR]; 0.8128[AMR]
rs7751598	rs1360780 rs9296158 rs9470080 rs3800373	intron_variant	0.8576[EUR]; 0.8349[AMR]
rs9394309	rs9470080	downstream_gene_variant; intron_variant	0.9161[EUR]
rs1591365	rs1360780 rs9296158 rs9470080 rs3800373	intron_variant	0.8576[EUR]
rs4713906	rs9470080	intron_variant	0.8921[EUR]
rs6457839	rs9470080	intron_variant	0.9039[EUR]
rs9394311	rs9470080	downstream_gene_variant; intron_variant	0.8835[EUR]; 0.8238[AMR]
rs4713911	rs9470080	downstream_gene_variant; intron_variant	0.8608[EUR]
rs9462103	rs9470080 rs4713916	5_prime_UTR_variant; intron_variant	0.8243[EUR]
rs10947563	rs9470080 rs4713916	intron_variant	0.8808[EUR]
rs6929523	rs9470080	intron_variant	0.8808[EUR]
rs9380525	rs1360780 rs9296158 rs9470080	upstream_gene_variant; intron_variant	1.0000[EUR]; 0.9511[AFR]; 0.8811[AMR]
rs2395634	rs1360780 rs9296158 rs9470080 rs3800373	intron_variant	0.8463[EUR]
rs9368881	rs1360780 rs9296158 rs9470080	upstream_gene_variant; intron_variant	1.0000[EUR]; 0.9592[AFR]; 0.8694[AMR]
rs7763535	rs9470080 rs4713916	intron_variant	0.8748[EUR]
rs6899478	rs9470080 rs4713916	intron_variant	0.8805[EUR]
rs9380526	rs1360780 rs9296158 rs9470080	upstream_gene_variant; intron_variant	0.9878[EUR]; 0.9115[AFR]; 0.9278[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
CRHR1	Yes	Adipose Subcutaneous	cis	GTEx