SNP Report

Basic Info

Name	rs4511180 dbSNP Ensembl
Location	1:202180311 - 202180311(+)
Variant Seq	G
Ancestral Allele	G
Ref Seq	A
Minor Allele Frequence	0.292931
Annotation	non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant
Variant Effect	non_coding_transcript_exon_variant(ENST00000482597); intron_variant(ENST00000490225); non_coding_transcript_variant(ENST00000490225, ENST00000482597)
SIFT Annotation	deleterious_-_low_confidence; tolerated_-_low_confidence; deleterious; tolerated
SIFT Variant Effect	deleterious_-_low_confidence(ENST00000435759, ENST00000309017, ENST00000480836, ENST00000486116, ENST00000496197); tolerated_-_low_confidence(ENST00000467283); deleterious(ENST00000462815, ENST00000629151); tolerated(ENST00000495688, ENST00000477554, ENST00000367279, ENST00000492451, ENST00000464870)
PolyPhen Annotation	benign; possibly_damaging
PolyPhen Variant Effect	benign(ENST00000495688, ENST00000467283, ENST00000309017, ENST00000477554, ENST00000486116, ENST00000367279, ENST00000492451, ENST00000464870); possibly_damaging(ENST00000462815, ENST00000435759, ENST00000480836, ENST00000496197, ENST00000629151)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Enhancers
No. of Marker's Association Results	1 (Positive: 0; Negative: 0; Trend: 1)
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 subjects of African: P-value=7.7E-07. In subjects of African: P-value=7.7E-07.	It met the threshold for suggestive evidence of association ...... It met the threshold for suggestive evidence of association (P-value<5E-06). More...	Trend

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	Gene and childhood trauma interaction: P-value<0.05 in any s...... Gene and childhood trauma interaction: P-value<0.05 in any subjects. 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)
PTPRVP	protein tyrosine phosphatase, receptor type V, pseudogene	1q32.1	1(0/0/1)

SNPs in LD with rs4511180 (count: 12)

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

rs3100127	downstream_gene_variant(ENST00000482597, ENST00000490225, ENST00000490575); upstream_gene_variant(ENST00000367278)	1(0/0/1)	0.9780[EUR]; 0.8612[AMR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs2924110	rs4511180 rs3100127	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9889[EUR]; 0.8078[AFR]; 0.9409[AMR]
rs2077566	rs4511180 rs3100127	intron_variant	0.9346[EUR]; 0.8498[AMR]
rs7525555	rs4511180 rs3100127	intron_variant; non_coding_transcript_variant	0.8414[EUR]; 0.8608[AMR]
rs3010090	rs4511180 rs3100127	intron_variant	0.9453[EUR]; 0.8498[AMR]
rs2361422	rs4511180 rs3100127	downstream_gene_variant; upstream_gene_variant	0.9889[EUR]; 0.9409[AMR]
rs2993427	rs4511180 rs3100127	upstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9235[AFR]; 0.9880[AMR]
rs10920357	rs4511180 rs3100127	upstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.8287[AFR]; 0.9762[AMR]
rs12410520	rs4511180 rs3100127	intron_variant; non_coding_transcript_variant	0.9310[EUR]; 0.8346[AMR]
rs2993426	rs4511180 rs3100127	intron_variant	0.9453[EUR]; 0.8498[AMR]
rs3120747	rs4511180 rs3100127	intron_variant	0.9780[EUR]; 0.9063[AMR]
rs10800820	rs4511180 rs3100127	intron_variant; non_coding_transcript_variant	0.8613[EUR]

SNP related eQTL (count: 1)

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