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.

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs4775277	rs16942660	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[AMR]
rs6494203	rs16942660	3_prime_UTR_variant; intron_variant; non_coding_transcript_variant	1.0000[AMR]
rs8028860	rs16942660	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[AFR]; 1.0000[AMR]
rs74020720	rs16942660	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8570[AFR]; 1.0000[AMR]
rs74017206	rs16942660	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[AMR]
rs74017207	rs16942660	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[AMR]

SNP related eQTL (count: 1)

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