SNP Report

Basic Info

Name	rs7954758 dbSNP Ensembl
Location	chr12:71942014 - 71942014(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.141374
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000333850, ENST00000546576); non_coding_transcript_variant(ENST00000546576)
No. of Studies	3 (Positive: 2; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Grigoroiu-Serbanescu, M.,2008	A/G		Cochrane-Armitage trend test P value=0.624 Cochrane-Armitage trend test P value=0.624		Negative
Gao, J., 2016			Fixed effect model: P-value=0.0044,Â OR=1.3597, 95%CI=1.1008...... Fixed effect model: P-value=0.0044,Â OR=1.3597, 95%CI=1.1008-1.6795; Random effects model: P-value=0.0887,Â OR=1.316, 95%CI=0.9592- 1.8068; More...	For rs7954758, three studies including 1081 BD patients and ...... For rs7954758, three studies including 1081 BD patients and 1480 controlswere included. All ethnic groups yielded a fixed effect summary OR of 1.36, without statistically significant between-study heterogeneity, while the random summary OR was 1.32 showed borderline statistical significance though it demonstrated a relatively poor association of rs7954758 with BD. It appeared that rs11178998 and rs4760820 had strong epidemiological credibility, while rs7954758 had relatively weak association due to significant between-study heterogeneity and failure to reach statistical significance in the random effective model. More...	Positive
Cichon, S., 2008	A/G	G	Cochrane-Armitage trend test P-value = 0.0039 , OR (95% CI)=...... Cochrane-Armitage trend test P-value = 0.0039 , OR (95% CI)=1.5 (1.1-1.9) in the German BPAD sample. Cochrane-Armitage trend test P-value = 0.0668 , OR (95% CI)=1.6 (0.96-2.6) in the Russian BPAD sample. Cochrane-Armitage trend test P-value = 0.0006 , OR (95% CI)=1.5 (1.2-1.9) in Combined German/Russian sample. More...	In the German sample, the minor alleles of SNPs rs11178997, ...... In the German sample, the minor alleles of SNPs rs11178997, rs11178998 and rs7954758 were significantly over-represented in BPAD patients when compared with controls. In the Russian replication sample, the three SNPs in the 5' region showed a non-signific. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
TPH2	tryptophan hydroxylase 2	12q15	13(10/3/0)

SNPs in LD with rs7954758 (count: 16) View in gBrowse (chr12:71867975..71944865 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 16)

rs_ID	Functional Annotation	r²[population]
rs7963717	upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs17110424	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.879[CEU]; 0.808[TSI]
rs7963803	upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs11178971	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.879[CEU]; 0.808[TSI]
rs7965232	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.879[CEU]; 0.808[TSI]
rs11178990	downstream_gene_variant	0.879[CEU]; 0.808[TSI]
rs11178988	3_prime_UTR_variant; downstream_gene_variant	0.879[CEU]; 0.808[TSI]
rs11179001	intron_variant; non_coding_transcript_variant	1.0[CEU]; 0.935[TSI]
rs11178989	3_prime_UTR_variant; downstream_gene_variant	0.879[CEU]
rs11178991		1.0[CEU]
rs11178992	upstream_gene_variant	1.0[CEU]
rs17110432	3_prime_UTR_variant; downstream_gene_variant	0.865[CEU]
rs11178993	upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs11178986	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.879[CEU]
rs17110426	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.879[CEU]; 0.808[TSI]
rs3815869	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.879[CEU]; 0.808[TSI]

Overlap with SZ from cross-disorder studies (count: 0)

Overlap with MDD from cross-disorder studies (count: 0)