PTSDgene database

SNP Report

Basic Info
Name rs12442490 dbSNP Ensembl
Location 15:61193166 - 61193166(+)
Variant Seq T
Ancestral Allele T
Ref Seq C
Minor Allele Frequence 0.207069
Annotation intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect intron_variant(ENST00000559145, ENST00000561093, ENST00000335670, ENST00000551975, ENST00000558904, ENST00000560300, ENST00000557822, ENST00000560876); NMD_transcript_variant(ENST00000551975); non_coding_transcript_variant(ENST00000559145, ENST00000561093, ENST00000560300, ENST00000557822, ENST00000560876)
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
No. of Marker's Association Results 1 (Positive: 1; Negative: 0; Trend: 0)
Source Literature

SNP related association results
Normal genetic study related association results (count: 1)
Reference Phenotype Statistical Values Author Comments Marker's Category
Nievergelt, C. M.,2015 PTSD In 2179 MRS subjects of European descent: P-value=0.003. In 2179 MRS subjects of European descent: P-value=0.003. P-value is nominally significant (P-value<0.05). P-value is nominally significant (P-value<0.05). Significant
G*E study related association result (count: 1)
Reference Phenotype Environment Statistical Values Author Comments Marker's Category
Nievergelt, C. M.,2015 PTSD Childhood trauma In 2179 MRS subjects of European descent, gene and childhood...... In 2179 MRS subjects of European descent, gene and childhood trauma interaction: P-value<0.05. More... It showed a non-significant interaction effect with childhoo...... It showed a non-significant interaction effect with childhood trauma on PTSD. More... Non-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 rs12442490 (count: 19)
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: 19)


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

Copyright: Key Lab of Mental Health, Institute of Psychology, Chinese Academy of Sciences Feedback
Last update: April 1, 2018