PTSDgene database

SNP Report

Basic Info
Name rs16942660 dbSNP Ensembl
Location 15:60508867 - 60508867(+)
Variant Seq T
Ancestral Allele C
Ref Seq C
Minor Allele Frequence 0.0341454
Annotation downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant
Variant Effect downstream_gene_variant(ENST00000559343, ENST00000551975, ENST00000560004); upstream_gene_variant(ENST00000559902); intron_variant(ENST00000501579, ENST00000558235, ENST00000335670, ENST00000261523, ENST00000449337, ENST00000309157, ENST00000558140, ENST00000559587, ENST00000559824); non_coding_transcript_variant(ENST00000501579, ENST00000558235, ENST00000558140, ENST00000559587, ENST00000559824)
SIFT Annotation tolerated
SIFT Variant Effect tolerated(ENST00000309157, ENST00000335670, ENST00000449337, ENST00000261523)
PolyPhen Annotation benign; possibly_damaging
PolyPhen Variant Effect benign(ENST00000335670, ENST00000261523); possibly_damaging(ENST00000309157, ENST00000449337)
rSNP? Yes Link in rVarBase
Related Regulatory Elements TF binding region;Chromatin interactive region
Chromatin State Weak transcription;Enhancers;Strong transcription;Genic 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 Increasing versus decreasing 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=3.13, P-value<0.05. More... rs16942660, having one or more copies of the minor allele wa...... rs16942660, having one or more copies of the minor allele was significantly associated with a greater likelihood of being in the increasing trajectory, relative to the decreasing trajectory. However, this result did not hold after correction for multiple testing. More... Significant
Logue, M. W.,2013 PTSD In the African-Americans from the DNHS sample: OR=2.65, Nom...... In the African-Americans from the DNHS sample: OR=2.65, Nominal P-value=0.00090, Adjusted P-value=0.202. More... In trauma-exposed African Americans from the DNHS, the most ...... In trauma-exposed African Americans from the DNHS, the most significant SNP associated with lifetime PTSD within RORA was rs16942660 633 kb from the peak SNP in African American's from the VA sample and 324 kb away from the peak SNP observed in the discovery sample of white non-Hispanic subjects. More... Non-significant


SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
RORA RAR related orphan receptor A 15q21-q22 6(4/2/0)
RORA-AS1 RORA antisense RNA 1 15q22.2 Mapped by Literature SNP, Mapped by LD-proxy

SNPs in LD with rs16942660 (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
RP11-259G18.3 No Adipose Subcutaneous cis GTEx