SNP Report

Basic Info

Name	rs1799978 dbSNP Ensembl
Location	11:113475629 - 113475629(+)
Variant Seq	C
Ancestral Allele	C
Ref Seq	T
Minor Allele Frequence	0.11901
Annotation	upstream_gene_variant; intron_variant; non_coding_transcript_variant
Variant Effect	upstream_gene_variant(ENST00000542616, ENST00000362072, ENST00000346454); intron_variant(ENST00000540600); non_coding_transcript_variant(ENST00000540600)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000362072, ENST00000543292, ENST00000538967, ENST00000544518, ENST00000542968, ENST00000346454)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000362072, ENST00000543292, ENST00000538967, ENST00000544518, ENST00000542968, ENST00000346454)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	TF binding region;CpG island
Chromatin State	Bivalent/Poised TSS;Flanking Bivalent TSS/Enh;Bivalent Enhancer;Active TSS;Flanking Active TSS;Enhancers
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
Duan, Z.,2015	PTSD diagnosis	Allele dose analysis model: P-value=0.61; Dominant effect: ...... Allele dose analysis model: P-value=0.61; Dominant effect: P-value=0.56; Recessive effect: P-value=0.41. More...	No significant results. No significant results.	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
DRD2	dopamine receptor D2	11q23.2	18(11/7/0)

SNPs in LD with rs1799978 (count: 11)

The LD data used here is based on 1000 Genome Phase I. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs4245152	rs1799978	upstream_gene_variant	0.8480[ASN]
rs4245151	rs1799978	upstream_gene_variant	0.8480[ASN]
rs12576653	rs1799978	upstream_gene_variant	0.8480[ASN]
rs4245153	rs1799978	upstream_gene_variant	0.8239[ASN]
rs12574578	rs1799978	upstream_gene_variant	0.8239[ASN]
rs4429089	rs1799978	upstream_gene_variant	0.8239[ASN]
rs7102650	rs1799978	intron_variant; non_coding_transcript_variant	0.9742[ASN]
rs6589382	rs1799978	upstream_gene_variant	0.8239[ASN]
rs73557296	rs1799978	intron_variant; non_coding_transcript_variant	0.9742[ASN]
rs12576181	rs1799978	upstream_gene_variant	0.8239[ASN]
rs60253148	rs1799978	intron_variant; non_coding_transcript_variant	0.9742[ASN]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
TRIM37	Yes	Adipose Subcutaneous	cis	GTEx