SNP Report

Basic Info

Name	rs544437 dbSNP Ensembl
Location	11:18044362 - 18044362(+)
Variant Seq	T
Ancestral Allele	C
Ref Seq	C
Minor Allele Frequence	0.358427
Annotation	upstream_gene_variant
Variant Effect	upstream_gene_variant(ENST00000250018, ENST00000528338, ENST00000417164)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000250018)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000250018)
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
Nievergelt, C. M.,2015	PTSD	In 2179 MRS subjects of European descent: P-value=0.25. In 2179 MRS subjects of European descent: P-value=0.25.	No significant result. No significant result.	Non-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: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
TPH1	tryptophan hydroxylase 1	11p15.3-p14	5(1/4/0)

SNPs in LD with rs544437 (count: 36)

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]

rs1799913	downstream_gene_variant(ENST00000528338); upstream_gene_variant(ENST00000525523, ENST00000525406); intron_variant(ENST00000417164, ENST00000250018); splice_region_variant(ENST00000417164, ENST00000250018); NMD_transcript_variant(ENST00000417164)	1(0/1/0)	0.8724[EUR]; 0.8775[AMR]

LD-proxies (count: 35)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs11024446	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8119[EUR]
rs211107	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9147[EUR]; 0.8881[AMR]
rs685657	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9147[EUR]; 0.8454[AMR]
rs1401163	rs1799913 rs544437	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8119[EUR]
rs10832872	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant	0.8467[EUR]
rs211108	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9147[EUR]; 0.8881[AMR]
rs685247	rs544437	intron_variant; NMD_transcript_variant	0.8028[EUR]
rs572940	rs1799913 rs544437	upstream_gene_variant	0.8619[EUR]; 0.8881[AMR]
rs2056246	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.8878[EUR]; 0.8559[AMR]
rs211106	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.8929[EUR]; 0.8160[AMR]
rs2237907	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.8724[EUR]; 0.8775[AMR]
rs2299625	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8119[EUR]
rs12292490	rs1799913 rs544437	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8020[EUR]
rs480425	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9147[EUR]; 0.8666[AMR]
rs1401164	rs1799913 rs544437	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8119[EUR]
rs593839	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9042[EUR]; 0.8241[AMR]
rs10741734	rs1799913 rs544437	non_coding_transcript_exon_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8624[EUR]; 0.8775[AMR]
rs2071532	rs1799913 rs544437	upstream_gene_variant	0.9416[EUR]; 0.8418[AMR]
rs546383	rs1799913 rs544437	upstream_gene_variant	0.9361[EUR]; 0.8686[AMR]
rs685249	rs544437	intron_variant; NMD_transcript_variant	0.8028[EUR]
rs7933505	rs1799913 rs544437	upstream_gene_variant; intron_variant; NMD_transcript_variant	0.8624[EUR]; 0.8563[AMR]
rs2191091	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8023[EUR]
rs169806	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9147[EUR]; 0.8454[AMR]
rs1607395	rs1799913 rs544437	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.8724[EUR]; 0.8775[AMR]
rs2237908	rs1799913 rs544437	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8467[EUR]
rs684302	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9147[EUR]; 0.8881[AMR]
rs72862028	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.8020[EUR]
rs508924	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.9147[EUR]; 0.8881[AMR]
rs887242	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8020[EUR]
rs1800532	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.8724[EUR]; 0.8775[AMR]
rs517005	rs1799913 rs544437	upstream_gene_variant	0.9301[EUR]
rs654734	rs1799913 rs544437	upstream_gene_variant	0.9147[EUR]; 0.8350[AMR]
rs652458	rs1799913 rs544437	upstream_gene_variant	0.9147[EUR]; 0.8881[AMR]
rs1518522	rs1799913 rs544437	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8466[EUR]; 0.8042[AMR]
rs10832874	rs1799913 rs544437	intron_variant; NMD_transcript_variant	0.8670[EUR]; 0.8253[AMR]

SNP related eQTL (count: 1)

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