SNP Report

Basic Info

Name	rs1049862 dbSNP Ensembl
Location	10:60029514 - 60029514(+)
Variant Seq	A
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.280152
Annotation	downstream_gene_variant; 3_prime_UTR_variant
Variant Effect	downstream_gene_variant(ENST00000489505, ENST00000480699, ENST00000503366, ENST00000618374, ENST00000355288, ENST00000502769, ENST00000612776); 3_prime_UTR_variant(ENST00000373827, ENST00000373820, ENST00000280772)
SIFT Annotation	tolerated_-_low_confidence
SIFT Variant Effect	tolerated_-_low_confidence(ENST00000263102)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000263102)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Enhancers;Flanking Active TSS
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
Logue, M. W.,2013	PTSD	OR=0.85, P-value=0.23, corrected P-value=1 OR=0.85, P-value=0.23, corrected P-value=1	The SNP was not associated with PTSD at the P-value<0.01 lev...... The SNP was not associated with PTSD at the P-value<0.01 level. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
ANK3	ankyrin 3, node of Ranvier (ankyrin G)	10q21	2(2/0/0)

SNPs in LD with rs1049862 (count: 4)

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]

rs12357206	intron_variant(ENST00000502769, ENST00000373820, ENST00000503366, ENST00000612776, ENST00000373827, ENST00000489505, ENST00000280772, ENST00000618374, ENST00000480699, ENST00000355288); non_coding_transcript_variant(ENST00000489505, ENST00000480699)	1(0/1/0)	0.9843[EUR]
rs11813307	intron_variant(ENST00000480699, ENST00000280772, ENST00000502769, ENST00000503366, ENST00000618374, ENST00000373827, ENST00000355288, ENST00000373820, ENST00000489505, ENST00000612776); non_coding_transcript_variant(ENST00000480699, ENST00000489505)	1(0/1/0)	0.8774[EUR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs10821657	rs1049862 rs12357206 rs11813307	intron_variant; non_coding_transcript_variant	0.8626[EUR]
rs11597421	rs1049862 rs12357206 rs11813307	intron_variant; non_coding_transcript_variant	0.8203[EUR]

SNP related eQTL (count: 1)

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