PTSDgene database

SNP Report

Basic Info
Name rs2242446 dbSNP Ensembl
Location 16:55656513 - 55656513(+)
Variant Seq T
Ancestral Allele C
Ref Seq C
Minor Allele Frequence 0.247005
Annotation 5_prime_UTR_variant; upstream_gene_variant; intron_variant
Variant Effect 5_prime_UTR_variant(ENST00000379906); upstream_gene_variant(ENST00000561820, ENST00000219833, ENST00000566163); intron_variant(ENST00000568529, ENST00000568943, ENST00000568655, ENST00000414754)
SIFT Annotation deleterious; tolerated
SIFT Variant Effect deleterious(ENST00000414754); tolerated(ENST00000379906, ENST00000566163, ENST00000561820, ENST00000219833, ENST00000568943, ENST00000568655, ENST00000568529)
PolyPhen Annotation possibly_damaging; probably_damaging
PolyPhen Variant Effect possibly_damaging(ENST00000568529); probably_damaging(ENST00000379906, ENST00000566163, ENST00000561820, ENST00000219833, ENST00000568943, ENST00000568655, ENST00000414754)
rSNP? Yes Link in rVarBase
Related Regulatory Elements TF binding region;CpG island
Chromatin State Bivalent/Poised TSS;Flanking Bivalent TSS/Enh;Bivalent Enhancer;Flanking Active TSS;Enhancers;Active TSS
No. of Marker's Association Results 13 (Positive: 4; Negative: 9; Trend: 0)
Source Literature

SNP related association results
Normal genetic study related association results (count: 13)
Reference Phenotype Statistical Values Author Comments Marker's Category
Pietrzak, R. H.,2015 Anxious arousal symptoms B=0.09, t=2.45, P-value=0.01 B=0.09, t=2.45, P-value=0.01 Rs2242446 genotype significantly predicted scale scores of ...... Rs2242446 genotype significantly predicted scale scores of anxious arousal symptoms. More... Significant
Pietrzak, R. H.,2015 Avoidance symptoms B=0.04, t=1.04, P-value=0.30 B=0.04, t=1.04, P-value=0.30 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 Count of anxious arousal symptoms B=0.12, t=3.04, P-value=0.002 B=0.12, t=3.04, P-value=0.002 Rs2242446 genotype significantly predicted count of anxious ...... Rs2242446 genotype significantly predicted count of anxious arousal symptoms. More... Significant
Pietrzak, R. H.,2015 Count of avoidance symptoms B=0.03, t=0.86, P-value=0.39 B=0.03, t=0.86, P-value=0.39 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 Count of dysphoric arousal symptoms B=0.05, t=1.36, P-value=0.17 B=0.05, t=1.36, P-value=0.17 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 Count of numbing symptoms B=0.01, t=0.29, P-value=0.78 B=0.01, t=0.29, P-value=0.78 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 Count of reexperiencing symptoms B=-0.00, t=0.01, P-value=0.99 B=-0.00, t=0.01, P-value=0.99 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 Dysphoric arousal symptoms B=0.06, t=1.69, P-value=0.09 B=0.06, t=1.69, P-value=0.09 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 Exaggerated Startle OR=1.76, t=3.24, P-value=0.001 OR=1.76, t=3.24, P-value=0.001 Rs2242446 genotype significantly predicted Exaggerated Start...... Rs2242446 genotype significantly predicted Exaggerated Startle symptom. More... Significant
Pietrzak, R. H.,2015 Hypervigilance OR=1.41, t=2.12, P-value=0.03 OR=1.41, t=2.12, P-value=0.03 Rs2242446 genotype significantly predicted Hypervigilance sy...... Rs2242446 genotype significantly predicted Hypervigilance symptom. More... Significant
Pietrzak, R. H.,2015 Numbing symptoms B=0.02, t=0.45, P-value=0.65 B=0.02, t=0.45, P-value=0.65 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 PCL total score B=0.04, t=1.16, P-value= 0.25 B=0.04, t=1.16, P-value= 0.25 No significant association observed. No significant association observed. Non-significant
Pietrzak, R. H.,2015 Reexperiencing symptoms B=0.01, t=0.17, P-value=0.87 B=0.01, t=0.17, P-value=0.87 No significant association observed. No significant association observed. Non-significant


SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
SLC6A2 solute carrier family 6 (neurotransmitter transporter), member 2 16q12.2 13(4/9/0)

SNPs in LD with rs2242446 (count: 6)
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: 6)


SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
RP11-707O23.5 No Adipose Subcutaneous cis GTEx