SNP Report

Basic Info

Name	rs2400707 dbSNP Ensembl
Location	5:148825489 - 148825489(+)
Variant Seq	G
Ancestral Allele	G
Ref Seq	A
Minor Allele Frequence	0.346446
Annotation	5_prime_UTR_variant
Variant Effect	5_prime_UTR_variant(ENST00000305988)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000305988)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000305988)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	TF binding region;Chromatin interactive region
Chromatin State	Enhancers;Flanking Active TSS;Active TSS;Weak transcription;Bivalent/Poised TSS
No. of Marker's Association Results	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 1)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Hauser, M. A.,2017	PTSD diagnosis	P-value>0.05 P-value>0.05	No main effects of rs2400707 on PTSD diagnosis were observed...... No main effects of rs2400707 on PTSD diagnosis were observed in either the NHB or NHW subset of our data set. More...	Non-significant

G*E study related association result (count: 5)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Hauser, M. A.,2017	PTSD diagnosis	Childhood trauma	Among the NHB cohort: P-value=0.038. Among the NHW cohort: P...... Among the NHB cohort: P-value=0.038. Among the NHW cohort: P-value=0.892. More...	The interaction with rs2400707 and childhood trauma was obse...... The interaction with rs2400707 and childhood trauma was observed among NMB participants but not observed among the NHW study participants. More...	Significant
Liberzon, I.,2014	Avoidance symptoms	Adverse childhood event (ACE)	Subscales of PTSD symptoms, avoidance symptoms: mean B=0.82,...... Subscales of PTSD symptoms, avoidance symptoms: mean B=0.82, SD=0.24, t=3.43, P-value=.0006. More...	All 3 subscales of PTSD symptoms showed rs2400707 x ACE inte...... All 3 subscales of PTSD symptoms showed rs2400707 x ACE interaction, including intrusive and hyperarousal; however, the subscale for avoidance symptoms had the most robust interaction. More...	Significant
Liberzon, I.,2014	Hyperarousal symptoms	Adverse childhood event (ACE)	Subscales of PTSD symptoms, hyperarousal: mean B=0.61, SD=0....... Subscales of PTSD symptoms, hyperarousal: mean B=0.61, SD=0.20, t=3.07, P-value=.002. More...	All 3 subscales of PTSD symptoms showed rs2400707 x ACE inte...... All 3 subscales of PTSD symptoms showed rs2400707 x ACE interaction, including intrusive and hyperarousal; however, the subscale for avoidance symptoms had the most robust interaction. More...	Significant
Liberzon, I.,2014	Intrusive symptoms	Adverse childhood event (ACE)	Subscales of PTSD symptoms, intrusive: mean B=0.47, SD=0.17,...... Subscales of PTSD symptoms, intrusive: mean B=0.47, SD=0.17, t=2.79, P-value=.005. More...	All 3 subscales of PTSD symptoms showed rs2400707 x ACE inte...... All 3 subscales of PTSD symptoms showed rs2400707 x ACE interaction, including intrusive and hyperarousal; however, the subscale for avoidance symptoms had the most robust interaction. More...	Significant
Liberzon, I.,2014	PTSD symptoms	Adverse childhood event (ACE)	Linear regression model controlling for adult trauma exposur...... Linear regression model controlling for adult trauma exposure, the SNP x ACE interaction: mean unstandardized estimate B= 3.07, SD=0.69, beta=0.243, t=4.48, P-value=1.02-5e. Stratification of the sample by ACEs in persons with 2 or more reported categories of ACEs:n=93, mean B =?6.44, SD=2.08, t=?3.10, P-value=.003. Secondary analysis of binary logistic regression of PTSD caseness: rs2400707 x ACE interaction: OR=0.54, P-value=5.16-4e. Addition of PCs of rs2400707: P-value=1.11-5e. The rs2407007 x ACE interaction in the association with PTSD symptoms in the Grady Trauma Project: mean B=1.80, SD=0.54, t=3.328, P-value=.0009; when using robust standard errors: mean B=1.81, SD=0.60, t=3.02, P-value=.0026 after controlling for sex and adult trauma exposure: mean B=1.58, SD=0.50, t=3.15, P-value=.0017 and after controlling for the 10 PCs: mean B=1.55, SD=0.51, t=3.06, P-value=.0022. In persons with 2 or more reported ACEs: n=197, mean B=?5.34, SD=1.35, t=3.95, P-value=.00011). More...	Significant associations were detected for the SNP x ACE int...... Significant associations were detected for the SNP x ACE interaction term in rs2400707. Permutation analysis of the SNP x ACE interaction term further confirmed a significant association with rs2400707 (P-value < .05 corrected for multiple comparisons). As shown in Figure 1A, rs2400707 AA homozygotes demonstrated lower levels of PTSD symptoms in the presence of 2 or more categories of reported childhood adversity in the discovery cohort. Stratification of the sample by ACEs showed an effect of rs2400707 only in persons with 2 or more reported categories of ACEs. Although our primary focus was on continuous measures of PTSD severity, a secondary analysis of binary logistic regression of PTSD caseness confirmed an rs2400707 x ACE interaction, indicating that the A allele is protective in terms of adult PTSD symptoms on categorical PTSD diagnosis. Addition of PCs did not alter the significant association of rs2400707. The rs2407007 x ACE interaction in the association with PTSD symptoms in the Grady Trauma Project remained significant when using robust standard errors after controlling for sex and adult trauma exposure and after controlling for the 10 PCs. Again, an effect of rs2400707 was found only in persons with 2 or more reported ACEs. We tested the same model (linear regression of SNP, ACEs, adult trauma, and SNP x ACE and SNP x adult trauma interaction terms) in the combined data set (adjusting symptom severity measures to the same scale) of both the discovery and replication cohorts. We found that the rs2400707 x ACE interaction term had a mean. More...	Significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
ADRB2	adrenoceptor beta 2	5q31-q32	1(0/1/0)

SNPs in LD with rs2400707 (count: 24)

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: 24)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs1042714	rs2400707	missense_variant; stop_gained	0.9675[EUR]
rs4705059	rs2400707	upstream_gene_variant	0.9040[EUR]; 0.8666[AFR]; 0.8879[AMR]
rs9325120	rs2400707	upstream_gene_variant	0.9678[EUR]; 0.9127[AFR]; 0.9619[AMR]
rs1801704	rs2400707	5_prime_UTR_variant	0.9515[EUR]
rs1042711	rs2400707	5_prime_UTR_variant	0.9515[EUR]
rs11168067	rs2400707	upstream_gene_variant	0.9946[EUR]; 0.9047[AFR]; 0.9872[AMR]
rs2053044	rs2400707	5_prime_UTR_variant	1.0000[EUR]; 0.9678[AFR]; 1.0000[AMR]
rs4705060	rs2400707	3_prime_UTR_variant	0.9040[EUR]; 0.8817[AFR]; 0.8997[AMR]
rs11746634	rs2400707	upstream_gene_variant	0.9946[EUR]; 0.9204[AFR]; 0.9872[AMR]
rs56330463	rs2400707	upstream_gene_variant	0.9568[EUR]; 0.9204[AFR]; 0.9496[AMR]
rs11958940	rs2400707	upstream_gene_variant	0.9891[EUR]; 0.9204[AFR]; 0.9744[AMR]
rs2082395	rs2400707	upstream_gene_variant	0.9891[EUR]; 0.9125[AFR]; 0.9744[AMR]
rs11959615	rs2400707	upstream_gene_variant	0.9837[EUR]; 0.9204[AFR]; 0.9744[AMR]
rs1432623	rs2400707	upstream_gene_variant	0.9946[EUR]; 0.9129[AFR]; 1.0000[AMR]
rs1432622	rs2400707	upstream_gene_variant	0.9946[EUR]; 0.9360[AFR]; 1.0000[AMR]
rs10078004	rs2400707	upstream_gene_variant	0.9249[EUR]; 0.9050[AFR]; 0.9492[AMR]
rs34064454	rs2400707	upstream_gene_variant	0.9891[EUR]; 0.9204[AFR]; 0.9744[AMR]
rs11959427	rs2400707	5_prime_UTR_variant	0.9729[EUR]
rs11168070	rs2400707	5_prime_UTR_variant	0.9783[EUR]
rs67339154	rs2400707	synonymous_variant	0.9249[EUR]; 0.9204[AFR]; 0.9492[AMR]
rs11168066	rs2400707	upstream_gene_variant	0.9891[EUR]; 0.9204[AFR]; 0.9744[AMR]
rs9325122	rs2400707	upstream_gene_variant	0.9464[EUR]
rs2082382	rs2400707	upstream_gene_variant	0.9409[EUR]
rs11168068	rs2400707	upstream_gene_variant	0.9946[EUR]; 0.9518[AFR]; 1.0000[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
CRHR1-IT1	Yes	Adipose Subcutaneous	cis	GTEx