SNP Report

Basic Info

Name	rs11178997 dbSNP Ensembl
Location	12:71938373 - 71938373(+)
Variant Seq	A
Ancestral Allele	T
Ref Seq	T
Minor Allele Frequence	0.151158
Annotation	upstream_gene_variant
Variant Effect	upstream_gene_variant(ENST00000333850, ENST00000546576)
SIFT Annotation	tolerated_-_low_confidence
SIFT Variant Effect	tolerated_-_low_confidence(ENST00000333850)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000333850)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	TF binding region;Chromatin interactive region
Chromatin State	Weak transcription
No. of Marker's Association Results	7 (Positive: 2; Negative: 5; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 7)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Cao, C.,2014	Anxious arousal symptoms	In total sample: t=-0.633, P-value=0.627, in females: t=0....... In total sample: t=-0.633, P-value=0.627, in females: t=0.544, P-value=0.587, in males: t=0.122, P-value=0.903. More...	No significant relationship. No significant relationship.	Non-significant
Cao, C.,2014	Avoidance symptoms	In total sample: t=0.422, P-value=0.039, in females: t=2.7...... In total sample: t=0.422, P-value=0.039, in females: t=2.765, P-value=0.006, in males: t=-0.364, P-value=0.717. More...	The rs11178997 'TT' genotype was significantly associated wi...... The rs11178997 'TT' genotype was significantly associated with avoidance symptoms in women but not in men. More...	Significant
Cao, C.,2014	Dysphoric arousal symptoms	In total sample: t=-0.406, P-value=0.642, in females: t=0....... In total sample: t=-0.406, P-value=0.642, in females: t=0.210, P-value=0.834, in males: t=0.414, P-value=0.680. More...	No significant relationship. No significant relationship.	Non-significant
Cao, C.,2014	Emotional numbing symptoms	In total sample: t=1.860, P-value=0.023, in females: t=2.5...... In total sample: t=1.860, P-value=0.023, in females: t=2.518, P-value=0.013, in males: t=0.539, P-value=0.592. More...	No significant relationship. No significant relationship.	Non-significant
Cao, C.,2014	PTSD symptoms	In total sample: t=0.082, P-value=0.133, in females: t=1.8...... In total sample: t=0.082, P-value=0.133, in females: t=1.807, P-value=0.072, in males: t=0.128, P-value=0.899. More...	No significant relationship. No significant relationship.	Non-significant
Goenjian, A. K.,2012	PTSD-RI (PTSD symptoms)	After adjusting for age, sex, exposure and environmental var...... After adjusting for age, sex, exposure and environmental variables, analyses of PTSD-RI and the 't' allele of TPH2 SNP rs11178997: X²=3.87, df=1, P-value=0.03. Lod score=0.02. More...	After adjusting for age, sex, exposure and environmental var...... After adjusting for age, sex, exposure and environmental variables, analyses indicated a significant association of PTSD-RI and the 't' allele of TPH2 SNP rs11178997. This gene explained 4% of the variance of PTSD-RI scores. More...	Significant
Cao, C.,2014	Reexperiencing symptoms	In total sample: t=-1.099, P-value=0.417, in females: t=1....... In total sample: t=-1.099, P-value=0.417, in females: t=1.231, P-value=0.220, in males: t=-0.304, P-value=0.762. More...	No significant relationship. No significant relationship.	Non-significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
TPH2	tryptophan hydroxylase 2	12q15	10(3/7/0)
TBC1D15	TBC1 domain family member 15	12q15	Mapped by LD-proxy, rSNP target

SNPs in LD with rs11178997 (count: 27)

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: 27)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs11178971	rs11178997	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8135[EUR]
rs7963717	rs11178997	upstream_gene_variant	1.0000[ASN]; 1.0000[EUR]
rs56124927	rs11178997	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.8871[EUR]
rs7965232	rs11178997	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs17110424	rs11178997	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs3759172	rs11178997	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs11178977	rs11178997	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8135[EUR]
rs11178996	rs11178997	upstream_gene_variant	1.0000[ASN]; 0.9633[EUR]
rs11178988	rs11178997	downstream_gene_variant; 3_prime_UTR_variant	0.8685[EUR]
rs11179001	rs11178997	intron_variant; non_coding_transcript_variant	0.9118[ASN]; 0.8693[EUR]
rs7963803	rs11178997	upstream_gene_variant	1.0000[ASN]; 1.0000[EUR]
rs58014153	rs11178997	upstream_gene_variant	1.0000[ASN]; 1.0000[EUR]
rs7954758	rs11178997	intron_variant; non_coding_transcript_variant	0.9614[ASN]; 0.9435[EUR]
rs11178992	rs11178997	upstream_gene_variant	1.0000[ASN]; 1.0000[EUR]
rs3815869	rs11178997	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs17110432	rs11178997	downstream_gene_variant; 3_prime_UTR_variant	0.8871[EUR]
rs17110426	rs11178997	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs11178993	rs11178997	upstream_gene_variant	1.0000[ASN]; 1.0000[EUR]
rs11178984	rs11178997	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs11178986	rs11178997	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs11178991	rs11178997	intron_variant; non_coding_transcript_variant	0.9871[ASN]; 1.0000[EUR]
rs11178989	rs11178997	downstream_gene_variant; 3_prime_UTR_variant	0.8871[EUR]
rs11178990	rs11178997	downstream_gene_variant	0.8871[EUR]
rs11178969	rs11178997	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8135[EUR]
rs7974296	rs11178997	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8871[EUR]
rs11178995	rs11178997	upstream_gene_variant	1.0000[ASN]; 1.0000[EUR]
rs11178998	rs11178997	5_prime_UTR_variant; upstream_gene_variant	1.0000[ASN]; 1.0000[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-707O23.5	No	Adipose Subcutaneous	cis	GTEx