SNP Report

Basic Info

Name	rs12939390 dbSNP Ensembl
Location	17:30308670 - 30308670(+)
Variant Seq	C
Ancestral Allele	C
Ref Seq	T
Minor Allele Frequence	0.325679
Annotation	upstream_gene_variant
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000584603, ENST00000261714, ENST00000578090, ENST00000577290)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000584603, ENST00000261714, ENST00000578090, ENST00000577290)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	Enhancers;Weak transcription
No. of Marker's Association Results	2 (Positive: 0; Negative: 2; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 2)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Solovieff, N.,2014	PTSD diagnosis	P-value=0.006 P-value=0.006	Achieved nominal levels of significance with PTSD diagnosis,...... Achieved nominal levels of significance with PTSD diagnosis, although was not significant after correction for multiple testing More...	Non-significant
Solovieff, N.,2014	PTSD severity	P-value=0.003 P-value=0.003	Achieved nominal levels of significance with PTSD severity, ...... Achieved nominal levels of significance with PTSD severity, although was not significant after correction for multiple testing More...	Non-significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
SLC6A4	solute carrier family 6 (neurotransmitter transporter), member 4	17q11.2	44(13/31/0)
GOSR1	golgi SNAP receptor complex member 1	17q11	rSNP target

SNPs in LD with rs12939390 (count: 22)

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: 22)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs8080149	rs12939390	upstream_gene_variant	0.9766[EUR]
rs35724800	rs12939390	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9650[EUR]
rs12941223	rs12939390	upstream_gene_variant	0.9766[EUR]
rs7223821	rs12939390	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9419[EUR]
rs1050565	rs12939390	missense_variant; non_coding_transcript_exon_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9419[EUR]
rs7208052	rs12939390	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9650[EUR]
rs3794806	rs12939390	intron_variant; NMD_transcript_variant	0.9650[EUR]
rs73268099	rs12939390	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.9650[EUR]
rs8078900	rs12939390	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.9593[EUR]
rs17767256	rs12939390	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9305[EUR]
rs33980254	rs12939390	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.9650[EUR]
rs36048853	rs12939390	upstream_gene_variant	0.9648[EUR]
rs12949747	rs12939390	intron_variant; NMD_transcript_variant	0.9650[EUR]
rs34353378	rs12939390	downstream_gene_variant	0.9883[EUR]
rs12938714	rs12939390	intron_variant	0.9883[EUR]
rs36000555	rs12939390	upstream_gene_variant	0.9707[EUR]
rs34622227	rs12939390	upstream_gene_variant	0.9707[EUR]
rs3764449	rs12939390	upstream_gene_variant	0.9766[EUR]
rs7342921	rs12939390	synonymous_variant; downstream_gene_variant; non_coding_transcript_exon_variant; 3_prime_UTR_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9650[EUR]
rs12947654	rs12939390	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8365[EUR]
rs12945042	rs12939390	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9089[EUR]
rs7214248	rs12939390	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8982[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
DND1P1	No	Adipose Subcutaneous	cis	GTEx