SNP Report

Basic Info

Name	rs16969968 dbSNP Ensembl
Location	15:78590583 - 78590583(+)
Variant Seq	A
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.149561
Annotation	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000559658, ENST00000348639, ENST00000559002, ENST00000326828); missense_variant(ENST00000299565); non_coding_transcript_exon_variant(ENST00000567141); intron_variant(ENST00000559554, ENST00000559576, ENST00000394802); non_coding_transcript_variant(ENST00000567141)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000299565)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000299565)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Strong transcription
No. of Marker's Association Results	1 (Positive: 0; Negative: 1; 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
Kimbrel, N. A.,2015	PTSD	Main genetic effects among NHB participants: P-value=0.0858...... Main genetic effects among NHB participants: P-value=0.0858, among the NHW participants: P-value=0.6153. More...	No main genetic effects were statistically significant among...... No main genetic effects were statistically significant among NHB participants at the multiple testing threshold of 0.0007 (Table 2). This SNP was also not associated with PTSD among the NHW participants. More...	Non-significant

G*E study related association result (count: 1)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Kimbrel, N. A.,2015	PTSD	Smoking status	GxE interactions among NHB participants: P-value=0.4467, amo...... GxE interactions among NHB participants: P-value=0.4467, among the NHW participants: P-value=0.172. More...	No GxE interactions were statistically significant among NHB...... No GxE interactions were statistically significant among NHB participants or among the NHW participants. More...	Non-significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
CHRNA3	cholinergic receptor, nicotinic alpha 3	15q24	1(0/1/0)
CHRNA5	cholinergic receptor, nicotinic alpha 5	15q24	2(1/1/0)

SNPs in LD with rs16969968 (count: 30)

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: 30)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs7172118	rs16969968	intron_variant	0.9772[EUR]; 0.9700[AMR]
rs72740955	rs16969968	intron_variant	0.9004[EUR]; 0.8522[AMR]
rs2036527	rs16969968	intron_variant	0.8952[EUR]; 0.8256[AMR]
rs72740964	rs16969968	upstream_gene_variant; intron_variant	0.9828[EUR]; 0.9848[AMR]
rs1317286	rs16969968	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9716[EUR]; 0.8266[AMR]
rs12914385	rs16969968	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8208[EUR]; 0.8266[AMR]
rs4887067	rs16969968	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9885[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs8034191	rs16969968	intron_variant; NMD_transcript_variant	0.8426[EUR]
rs8031948	rs16969968	intron_variant; NMD_transcript_variant	0.8586[EUR]
rs951266	rs16969968	downstream_gene_variant; upstream_gene_variant; intron_variant	0.9772[EUR]; 0.9700[AMR]
rs7180002	rs16969968	intron_variant	0.9772[EUR]; 0.9700[AMR]
rs17486278	rs16969968	intron_variant	0.9772[EUR]; 0.9138[AMR]
rs11633958	rs16969968	intron_variant	0.9715[EUR]; 0.9848[AMR]
rs17486195	rs16969968	intron_variant	0.9772[EUR]; 0.9700[AMR]
rs931794	rs16969968	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant	0.8487[EUR]
rs4243084	rs16969968	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9549[EUR]
rs56390833	rs16969968	downstream_gene_variant; intron_variant	0.9658[EUR]; 0.9700[AMR]
rs8192482	rs16969968	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9885[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs55676755	rs16969968	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9772[EUR]; 0.9554[AMR]
rs55853698	rs16969968	5_prime_UTR_variant	0.9056[EUR]
rs17487223	rs16969968	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8340[EUR]
rs2869548	rs16969968	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.8197[EUR]
rs55958997	rs16969968	downstream_gene_variant; upstream_gene_variant	0.8214[EUR]
rs1051730	rs16969968	synonymous_variant; non_coding_transcript_exon_variant; upstream_gene_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9772[EUR]; 0.9413[AMR]
rs58365910	rs16969968	downstream_gene_variant	0.8844[EUR]; 0.8002[AMR]
rs72738786	rs16969968	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant	0.8631[EUR]
rs10519203	rs16969968	intron_variant; NMD_transcript_variant	0.8431[EUR]
rs56077333	rs16969968	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8674[EUR]; 0.8522[AMR]
rs8039449	rs16969968	downstream_gene_variant; upstream_gene_variant	0.8326[EUR]
rs55781567	rs16969968	5_prime_UTR_variant	0.9004[EUR]

SNP related eQTL (count: 1)

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