PTSDgene database

SNP Report

Basic Info
Name rs893290 dbSNP Ensembl
Location 15:61190958 - 61190958(+)
Variant Seq T
Ancestral Allele T
Ref Seq G
Minor Allele Frequence 0.0395367
Annotation intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect intron_variant(ENST00000560300, ENST00000335670, ENST00000557822, ENST00000551975, ENST00000560876, ENST00000558904, ENST00000559145, ENST00000561093); NMD_transcript_variant(ENST00000551975); non_coding_transcript_variant(ENST00000560300, ENST00000557822, ENST00000560876, ENST00000559145, ENST00000561093)
SIFT Annotation deleterious_-_low_confidence; tolerated
SIFT Variant Effect deleterious_-_low_confidence(ENST00000551975); tolerated(ENST00000335670)
PolyPhen Annotation benign; possibly_damaging
PolyPhen Variant Effect benign(ENST00000335670); possibly_damaging(ENST00000551975)
rSNP? Yes Link in rVarBase
Related Regulatory Elements n/a
Chromatin State Weak transcription;Enhancers
No. of Marker's Association Results 2 (Positive: 1; Negative: 1; Trend: 0)
Source Literature

SNP related association results
Normal genetic study related association results (count: 2)
Reference Phenotype Statistical Values Author Comments Marker's Category
Lowe, S. R.,2015 High versus low posttraumatic stress trajectory Main effects of RORA SNPs on trajectory membership (controll...... Main effects of RORA SNPs on trajectory membership (controlling for age, gender, and ancestry): OR=3.64, P-value<0.01. More... For rs893290, having one or more copies of the minor allele ...... For rs893290, having one or more copies of the minor allele was associated with a greater likelihood of being in the high trajectory, relative to the low trajectory, a result that remained significant after correction for multiple testing. More... Significant
Logue, M. W.,2013 PTSD In the African-Americans from the DNHS sample: OR=1.85, Nom...... In the African-Americans from the DNHS sample: OR=1.85, Nominal P-value=0.0052, Adjusted P-value=0.698. More... Non-significant
G*E study related association result (count: 3)
Reference Phenotype Environment Statistical Values Author Comments Marker's Category
Lowe, S. R.,2015 Decreasing versus low posttraumatic stress trajectory Childhood physical abuse Interaction between rs893290 and childhood physical abuse: O...... Interaction between rs893290 and childhood physical abuse: OR=1.22, P-value<0.05. More... The interaction between rs893290 and childhood physical abus...... The interaction between rs893290 and childhood physical abuse was significantly predictive of membership in the decreasing trajectories, relative to the low trajectory. With correction for multiple testing, the interaction remained a significant predictor of decreasing trajectories, relative to the low trajectory. More... Significant
Lowe, S. R.,2015 High versus low posttraumatic stress trajectory Childhood physical abuse Interaction between rs893290 and childhood physical abuse: O...... Interaction between rs893290 and childhood physical abuse: OR=1.32, P-value<0.05. More... The interaction between rs893290 and childhood physical abus...... The interaction between rs893290 and childhood physical abuse was significantly predictive of membership in the high trajectories, relative to the low trajectory. With correction for multiple testing, the interaction remained a significant predictor of high trajectories, relative to the low trajectory. More... Significant
Lowe, S. R.,2015 Increasing versus low posttraumatic stress trajectory Childhood physical abuse Interaction between rs893290 and childhood physical abuse: O...... Interaction between rs893290 and childhood physical abuse: OR=1.46, P-value<0.05. More... The interaction between rs893290 and childhood physical abus...... The interaction between rs893290 and childhood physical abuse was significantly predictive of membership in the increasing trajectories, relative to the low trajectory. More... Significant


SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
RORA RAR related orphan receptor A 15q21-q22 6(4/2/0)

SNPs in LD with rs893290 (count: 5)
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: 5)


SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
RP11-259G18.3 No Adipose Subcutaneous cis GTEx