SNP Report

Basic Info

Name	rs1928040 dbSNP Ensembl
Location	chr13:46873101 - 46873101(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	G
Minor Allele Frequence	0.449481
Functional Annotation	intron_variant.
Consequence to Transcript	intron_variant(ENST00000378688, ENST00000542664, ENST00000543956)
No. of Studies	2 (Positive: 0; Negative: 2; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	YES

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
McAuley, E. Z.,2009			single marker association: Asymptotic P-value = 0.17, Empiri...... single marker association: Asymptotic P-value = 0.17, Empirical P-value = 0.17, Odds ratio=0.82 More...	No significant allelic association with BP was found No significant allelic association with BP was found	Negative
Kishi, T.,2009(b)	T/C		chi-square test: 1.total samples: P-value = 0.287(Genotype),...... chi-square test: 1.total samples: P-value = 0.287(Genotype), P-value = 0.182(Allele) in BP 2. male samples: P-value = 0.592(Genotype), P-value = 0.307(Allele) in BP 3. female samples: P-value = 0.436(Genotype), P-value = 0.374(Allele) in BP More...	No significant association was observed No significant association was observed	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HTR2A	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	13q14-q21	22(7/15/0)

SNPs in LD with rs1928040 (count: 19) View in gBrowse (chr13:46864839..46901159 )

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

rs_ID	Functional Annotation	r²[population]
rs9316235	intron_variant	0.841[JPT]
rs4941573	downstream_gene_variant; intron_variant	0.888[CEU]; 0.933[TSI]
rs9567743	intron_variant	0.841[JPT]
rs2770293	intron_variant	0.826[CHD]
rs9526246	intron_variant	0.958[CEU]
rs732821	upstream_gene_variant	0.812[CEU]
rs2770297	intron_variant	0.892[CHB]; 0.854[CHD]; 1.0[JPT]
rs4941575	upstream_gene_variant	0.884[CEU]
rs582854	intron_variant	0.826[CHD]; 0.841[JPT]
rs2770298	intron_variant	0.892[CHB]; 0.854[CHD]; 1.0[JPT]
rs9567746	intron_variant	0.841[JPT]
rs6561336	intron_variant	0.924[CEU]; 0.911[TSI]
rs9562688	intron_variant	0.841[JPT]
rs9562687	intron_variant	0.841[JPT]
rs9534513	upstream_gene_variant	0.835[CEU]
rs731779	intron_variant	0.841[JPT]
rs4941570	intron_variant	0.913[CEU]
rs731245	upstream_gene_variant	0.812[CEU]
rs9526245	intron_variant	0.841[JPT]

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

Overlap with MDD from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Kishi, T.,2009(b)	chi-square test: 1.total samples:P-value = 0.894(Genotype), P-value = 0.888(Allele) in Mood disorders;P-value = 0.370(Genotype), P-value = 0.499(Allele) in MDD 2. male samples: P-value = 0.929(Genotype), P-value = 0.977(Allele) in Mood disorders;P-value = 0.623(Genotype), P-value = 0.524(Allele) in MDD 3. female samples: P-value = 0.930(Genotype), P-value = 0.837(Allele) in Mood disorders;P-value = 0.551(Genotype), P-value = 0.771(Allele) in MDD	we did not detect any significant association of HTR2A with MDD or BP in allele/genotype-wise analysis.	Negative