SNP Report

Basic Info

Name	rs6279 dbSNP Ensembl
Location	11:113410351 - 113410351(+)
Variant Seq	C
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.478235
Annotation	downstream_gene_variant; 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000538967, ENST00000539420, ENST00000540600, ENST00000535984); 3_prime_UTR_variant(ENST00000544518, ENST00000542968, ENST00000346454, ENST00000362072); intron_variant(ENST00000546284); non_coding_transcript_variant(ENST00000546284)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000538967, ENST00000544518, ENST00000362072, ENST00000542968)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000538967, ENST00000544518, ENST00000362072, ENST00000542968)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription
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=0.29; Dominant effect: ...... Allele dose analysis model: P-value=0.29; Dominant effect: P-value=0.32; Recessive effect: P-value=0.15. 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 rs6279 (count: 28)

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: 1)

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

rs1124492	downstream_gene_variant(ENST00000539420, ENST00000535984, ENST00000540600); non_coding_transcript_exon_variant(ENST00000546284); intron_variant(ENST00000544518, ENST00000542968, ENST00000346454, ENST00000538967, ENST00000362072); non_coding_transcript_variant(ENST00000546284)	1(0/1/0)	0.8566[ASN]

LD-proxies (count: 27)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs11214598	rs6279	intron_variant; NMD_transcript_variant	0.9580[ASN]
rs11214602	rs6279	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9859[ASN]
rs4938014	rs1124492 rs6279	intron_variant; NMD_transcript_variant	0.8190[ASN]
rs4590907	rs1124492 rs6279	upstream_gene_variant; intron_variant	0.8132[ASN]
rs2587543	rs6279	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs4938016	rs6279	downstream_gene_variant; missense_variant	0.9580[ASN]
rs2245805	rs6279	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9314[ASN]
rs12224538	rs1124492 rs6279	upstream_gene_variant; intron_variant	0.8132[ASN]
rs2734841	rs6279	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs2859544	rs6279	downstream_gene_variant; upstream_gene_variant	0.9789[ASN]
rs2242592	rs6279	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs2005313	rs6279	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9314[ASN]
rs2859543	rs6279	downstream_gene_variant; upstream_gene_variant	0.9789[ASN]
rs2734842	rs6279	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs2002453	rs6279	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9314[ASN]
rs6276	rs6279	downstream_gene_variant; 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs1124493	rs6279	downstream_gene_variant; non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs2587550	rs6279	downstream_gene_variant; upstream_gene_variant	0.9789[ASN]
rs2511521	rs6279	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9380[ASN]
rs1076562	rs6279	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9244[ASN]
rs1003641	rs6279	downstream_gene_variant; upstream_gene_variant	0.9789[ASN]
rs2587552	rs6279	downstream_gene_variant; upstream_gene_variant	0.9789[ASN]
rs61492892	rs1124492 rs6279	upstream_gene_variant; intron_variant	0.8132[ASN]
rs2471856	rs4586205 rs6279	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9039[ASN]
rs2859545	rs6279	downstream_gene_variant; upstream_gene_variant	0.9649[ASN]
rs7122228	rs6279	downstream_gene_variant; intron_variant	0.9580[ASN]
rs6275	rs6279	synonymous_variant; downstream_gene_variant	0.9653[ASN]

SNP related eQTL (count: 1)

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