SNP Report

Basic Info

Name	rs363238 dbSNP Ensembl
Location	10:117279248 - 117279248(+)
Variant Seq	A
Ancestral Allele	C
Ref Seq	C
Minor Allele Frequence	0.221845
Annotation	non_coding_transcript_exon_variant; 3_prime_UTR_variant; non_coding_transcript_variant
Variant Effect	non_coding_transcript_exon_variant(ENST00000497497); 3_prime_UTR_variant(ENST00000298472, ENST00000334464); non_coding_transcript_variant(ENST00000497497)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000334464)
PolyPhen Annotation	probably_damaging
PolyPhen Variant Effect	probably_damaging(ENST00000334464)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Strong transcription
No. of Marker's Association Results	1 (Positive: 1; Negative: 0; 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
Nievergelt, C. M.,2015	PTSD	In 2179 MRS subjects of European descent: P-value=0.022. In 2179 MRS subjects of European descent: P-value=0.022.	P-value is nominally significant (P-value<0.05). P-value is nominally significant (P-value<0.05).	Significant

G*E study related association result (count: 1)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Nievergelt, C. M.,2015	PTSD	Childhood trauma	In 2179 MRS subjects of European descent, gene and childhood...... In 2179 MRS subjects of European descent, gene and childhood trauma interaction: P-value<0.05. More...	It showed a non-significant interaction effect with childhoo...... It showed a non-significant interaction effect with childhood trauma on PTSD. More...	Non-significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
SLC18A2	solute carrier family 18 (vesicular monoamine transporter), member 2	10q25	3(2/1/0)
PDZD8	PDZ domain containing 8	10q26.12	Mapped by Literature SNP, Mapped by LD-proxy, rSNP target

SNPs in LD with rs363238 (count: 35)

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: 35)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs2283142	rs363238	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8970[AMR]
rs363228	rs363238	non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant	0.9874[EUR]; 0.9031[AMR]
rs12221325	rs363238	intron_variant; non_coding_transcript_variant	0.8636[AMR]
rs363296	rs363238	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8636[AMR]
rs72825515	rs363238	upstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9402[AFR]; 1.0000[AMR]
rs4752048	rs363238	intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9546[AFR]; 1.0000[AMR]
rs363271	rs363238	non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant	0.9874[EUR]; 0.9031[AMR]
rs1860407	rs363238	upstream_gene_variant	0.8767[EUR]; 0.8387[AFR]
rs12250377	rs363238	intron_variant; non_coding_transcript_variant	0.8970[AMR]
rs10082478	rs363238	upstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9402[AFR]; 1.0000[AMR]
rs10886062	rs363238	intron_variant; non_coding_transcript_variant	0.9007[EUR]; 0.8957[AFR]; 0.8647[AMR]
rs2153714	rs363238	synonymous_variant; upstream_gene_variant	0.8767[EUR]
rs2532809	rs363238	non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant	0.9874[EUR]; 0.9031[AMR]
rs363279	rs363238	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8636[AMR]
rs363227	rs363238	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9874[EUR]; 0.9031[AMR]
rs4752056	rs363238	5_prime_UTR_variant; upstream_gene_variant	0.8767[EUR]
rs10082507	rs363238	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8636[AMR]
rs59602484	rs363238	intron_variant; non_coding_transcript_variant	0.8636[AMR]
rs10886058	rs363238	intron_variant; non_coding_transcript_variant	0.9751[EUR]; 0.9546[AFR]; 1.0000[AMR]
rs11197945	rs363238	intron_variant; non_coding_transcript_variant	0.8636[AMR]
rs363262	rs363238	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8636[AMR]
rs12244411	rs363238	intron_variant; non_coding_transcript_variant	0.8767[EUR]; 0.8806[AFR]; 0.8647[AMR]
rs11197938	rs363238	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8134[AMR]
rs10787767	rs363238	intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9546[AFR]; 1.0000[AMR]
rs12571779	rs363238	intron_variant; non_coding_transcript_variant	0.9251[EUR]; 0.8957[AFR]; 0.8976[AMR]
rs2901123	rs363238	intron_variant; non_coding_transcript_variant	0.9007[EUR]; 0.8957[AFR]; 0.8647[AMR]
rs887341	rs363238	intron_variant; non_coding_transcript_variant	0.8546[EUR]; 0.8957[AFR]; 0.8647[AMR]
rs12414644	rs363238	intron_variant; non_coding_transcript_variant	0.9251[EUR]; 0.8687[AFR]; 0.8976[AMR]
rs363303	rs363238	intron_variant; non_coding_transcript_variant	0.9874[EUR]; 0.9182[AMR]
rs363229	rs363238	non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant	0.9874[EUR]; 0.9031[AMR]
rs12569963	rs363238	intron_variant; non_coding_transcript_variant	0.8957[AFR]
rs363272	rs363238	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9874[EUR]; 0.9031[AMR]
rs10787771	rs363238	upstream_gene_variant	0.8767[EUR]; 0.8109[AFR]
rs12265713	rs363238	intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9402[AFR]; 1.0000[AMR]
rs2255321	rs363238	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9827[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-259G18.3	No	Adipose Subcutaneous	cis	GTEx