SNP Report

Basic Info

Name	rs878567 dbSNP Ensembl
Location	chr5:63960164 - 63960164(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.352236
Functional Annotation	downstream_gene_variant; intron_variant; non_coding_transcript_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000323865, ENST00000506598); intron_variant(ENST00000502882); non_coding_transcript_variant(ENST00000502882)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Kishi, T.,2012(a)			BP: all P-value > 0.05 BP: all P-value > 0.05	No significant association was observed. No significant association was observed.	Negative
Kishi, T.,2011(b)	C>T		For BD, chi-square tests: genotype, P-value = 0.00000183, co...... For BD, chi-square tests: genotype, P-value = 0.00000183, corrected P-value = 0.000022; allele, P-value = 0.00000212, corrected P-value = 0.0000254 More...	Significant associations were found in both allele and genot...... Significant associations were found in both allele and genotype association. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HTR1A	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	5q11.2-q13	3(2/1/0)

SNPs in LD with rs878567 (count: 20) View in gBrowse (chr5:63926954..64061731 )

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]
rs358524		0.833[CHB]; 1.0[CHD]
rs358528		0.911[CHB]; 1.0[CHD]
rs6859392		0.911[CHB]
rs1549274		0.911[CHB]; 1.0[CHD]
rs421321		0.904[CHB]; 0.845[CHD]
rs6878612	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs6449693	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs358533		0.911[CHB]; 1.0[CHD]
rs6871991		0.911[CHB]
rs10085024		1.0[CHB]; 1.0[JPT]
rs11954238		0.911[CHB]
rs12653018	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs2161615		0.911[CHB]
rs1182949		0.897[CHB]
rs4521432	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs10042486	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1423691	downstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs356612		0.813[CHB]; 0.845[CHD]
rs378864		0.904[CHB]; 0.845[CHD]
rs382098		0.904[CHB]; 0.845[CHD]

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

Reference	Statistical Result	Description	Result Category
Kishi, T.,2011(b)	For SZ, chi-square tests:genotype, P-value = 0.0606, corrected P-value = 0.286;allele, P-value = 0.0238	No significant association was observed.	Negative

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

Reference	Statistical Result	Description	Result Category
Kishi, T.,2012(a)	Meta analysis:P (allele model) = 0.0007 and P (dominant model) = 0.01	Significant association was found.	Positive