SNP Report

Basic Info

Name	rs6494223 dbSNP Ensembl
Location	chrCHR_HSCHR15_4_CTG8:32255110 - 32255110(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.46266
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000636184, ENST00000636295); intron_variant(ENST00000306901, ENST00000437966, ENST00000454250, ENST00000635722, ENST00000635759, ENST00000635884, ENST00000635978, ENST00000636044, ENST00000636271, ENST00000636440, ENST00000636603, ENST00000636647, ENST00000636850, ENST00000637033, ENST00000637183, ENST00000637350, ENST00000637519, ENST00000637552, ENST00000637786, ENST00000637971, ENST00000638031, ENST00000638106); NMD_transcript_variant(ENST00000437966, ENST00000635722, ENST00000635759, ENST00000636044, ENST00000636271, ENST00000636850, ENST00000637350, ENST00000637519, ENST00000637786, ENST00000637971, ENST00000638031); non_coding_transcript_variant(ENST00000636647, ENST00000455693)
No. of Studies	2 (Positive: 0; Negative: 2; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Joo, E. J.,2010	C/T		Association analysis: allele P-value > 0.05, genotype P-valu...... Association analysis: allele P-value > 0.05, genotype P-value > 0.05 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Ancin, I.,2011(a)	C/T		Genotypic analysis, in subjects who carried out CPT-DS, X Genotypic analysis, in subjects who carried out CPT-DS, X²=4.2, P-value = 0.12 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)
CHRNA7	cholinergic receptor, nicotinic, alpha 7 (neuronal)	15q13.3	4(2/2/0)

SNPs in LD with rs6494223 (count: 5) View in gBrowse (chrCHR_HSCHR15_4_CTG8:32244100..32255374 )

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]
rs8029400	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs4779565	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.802[CHD]; 0.804[JPT]
rs7175581	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.954[CHB]; 0.948[CHD]; 0.846[JPT]
rs12438848	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.804[JPT]
rs8028396	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Joo, E. J.,2010	Association analysis:allele P-value > 0.05, genotype P-value > 0.05	No significant association was observed.	Negative

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