SNP Report

Basic Info

Name	rs6269 dbSNP Ensembl
Location	22:19962429 - 19962429(+)
Variant Seq	G
Ancestral Allele	G
Ref Seq	A
Minor Allele Frequence	0.356829
Annotation	5_prime_UTR_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect	5_prime_UTR_variant(ENST00000403710); upstream_gene_variant(ENST00000493893, ENST00000449653, ENST00000428707, ENST00000585066); intron_variant(ENST00000407537, ENST00000467943, ENST00000207636, ENST00000412786, ENST00000361682, ENST00000403184, ENST00000406520); NMD_transcript_variant(ENST00000207636); non_coding_transcript_variant(ENST00000467943)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000361682, ENST00000412786, ENST00000403184, ENST00000403710, ENST00000449653, ENST00000207636, ENST00000406520, ENST00000407537)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000361682, ENST00000412786, ENST00000403184, ENST00000403710, ENST00000449653, ENST00000207636, ENST00000406520, ENST00000407537)
rSNP?	No Link in rVarBase
Related Regulatory Elements	N.A.
Chromatin State	N.A.
No. of Marker's Association Results	4 (Positive: 0; Negative: 4; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 4)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Goenjian, A. K.,2014	B category score	Trait DSM-IV based and DSM-V based: both with P-value>0.05. Trait DSM-IV based and DSM-V based: both with P-value>0.05.	There was no significant association between this SNP and su...... There was no significant association between this SNP and subcategory scores, and either of the total PTSD scores. More...	Non-significant
Goenjian, A. K.,2014	C category score	Trait DSM-IV based and DSM-V based: both with P-value>0.05. Trait DSM-IV based and DSM-V based: both with P-value>0.05.	There was no significant association between this SNP and su...... There was no significant association between this SNP and subcategory scores, and either of the total PTSD scores. More...	Non-significant
Goenjian, A. K.,2014	D category score	Trait DSM-IV based and DSM-V based: both with P-value>0.05. Trait DSM-IV based and DSM-V based: both with P-value>0.05.	There was no significant association between this SNP and su...... There was no significant association between this SNP and subcategory scores, and either of the total PTSD scores. More...	Non-significant
Goenjian, A. K.,2014	Total PTSD symptom severity score	Trait DSM-IV based and DSM-V based: both with P-value>0.05. Trait DSM-IV based and DSM-V based: both with P-value>0.05.	There was no significant association between this SNP and su...... There was no significant association between this SNP and subcategory scores, and either of the total PTSD scores. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
COMT	catechol-O-methyltransferase	22q11.21	21(9/12/0)

SNPs in LD with rs6269 (count: 7)

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]

rs4818	downstream_gene_variant(ENST00000467943); synonymous_variant(ENST00000406520, ENST00000412786, ENST00000403710, ENST00000361682, ENST00000449653, ENST00000407537, ENST00000207636, ENST00000403184); non_coding_transcript_exon_variant(ENST00000493893); upstream_gene_variant(ENST00000428707, ENST00000585066); NMD_transcript_variant(ENST00000207636); non_coding_transcript_variant(ENST00000493893)	4(0/4/0)	0.9621[EUR]

LD-proxies (count: 6)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs2239393	rs4818 rs6269	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	1.0000[EUR]
rs9306234	rs6269	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.8031[EUR]
rs3810595	rs4818 rs6269	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[EUR]
rs4646317	rs4818 rs6269	downstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant	0.8732[EUR]
rs740601	rs4818 rs6269	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	1.0000[EUR]
rs4646312	rs4818 rs6269	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9622[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
FBLL1	No	Adipose Subcutaneous	cis	GTEx