SNP Report

Basic Info

Name	rs6438552 dbSNP Ensembl
Location	chr3:119912967 - 119912967(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.40655
Functional Annotation	intron_variant.
Consequence to Transcript	intron_variant(ENST00000264235, ENST00000316626)
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
Lin YF, 2013	C/T		Chi square test:genotype,P-value = 0.399,chi square = 1.839;...... Chi square test:genotype,P-value = 0.399,chi square = 1.839;allele,P-value = 0.959,chi square = 0.003 More...	No significant association was observed. No significant association was observed.	Negative
Saus, E.,2010	A/G		association analyses with diagnosis: codominant P-value = 0....... association analyses with diagnosis: codominant P-value = 0.339, dominant P-value = 0.219, recessive P-value = 0.702, additive P-value = 0.517 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
GSK3B	glycogen synthase kinase 3 beta	3q13.3	8(0/8/0)

SNPs in LD with rs6438552 (count: 56) View in gBrowse (chr3:119814409..120092721 )

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: 56)

rs_ID	Functional Annotation	r²[population]
rs334563	intron_variant	0.907[CHB]; 1.0[CHD]; 1.0[JPT]
rs6784598	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.954[CHB]; 0.951[CHD]; 0.86[JPT]
rs17204878	intron_variant	0.907[CHB]; 1.0[CHD]; 1.0[JPT]
rs4688046	intron_variant	0.867[JPT]
rs10433404	intron_variant	0.867[JPT]
rs1870931	intron_variant; upstream_gene_variant	0.867[JPT]
rs9878473	intron_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs10934500	intron_variant; non_coding_transcript_variant	0.867[JPT]
rs12634476	intron_variant	0.867[JPT]
rs12634889	intron_variant; upstream_gene_variant	0.861[JPT]
rs6785049	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.954[CHB]; 0.976[CHD]; 0.908[JPT]
rs2319398	intron_variant	0.954[CHB]; 1.0[CHD]; 1.0[JPT]
rs11915717	intron_variant	0.826[JPT]
rs3107669	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2319399	intron_variant	0.954[CHB]; 1.0[CHD]; 1.0[JPT]
rs4340737	intron_variant	0.867[JPT]
rs7644234	intron_variant	0.907[CHB]; 1.0[CHD]; 1.0[JPT]
rs4688054	intron_variant	0.867[JPT]
rs1719894	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4624596	intron_variant; non_coding_transcript_variant	0.867[JPT]
rs9873477	intron_variant	0.954[CHB]; 1.0[CHD]; 1.0[JPT]
rs2199503	intron_variant	0.907[JPT]
rs9813864	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs10934505	intron_variant	0.867[JPT]
rs12629015	intron_variant	0.863[CHB]; 0.867[JPT]
rs7633279	intron_variant; non_coding_transcript_variant	0.867[JPT]
rs10934507	intron_variant	0.846[JPT]
rs6792572	intron_variant	0.954[CHB]; 1.0[CHD]; 1.0[JPT]
rs6782799	intron_variant	0.951[CHB]; 0.95[JPT]
rs12638973	intron_variant	0.853[JPT]
rs3732361	3_prime_UTR_variant; downstream_gene_variant	1.0[CHB]; 0.951[CHD]; 0.86[JPT]
rs6800622	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs10934506	intron_variant	0.867[JPT]
rs6781942	intron_variant; upstream_gene_variant	0.907[CHB]; 1.0[JPT]
rs2873950	intron_variant; non_coding_transcript_variant	0.817[JPT]
rs6805251	intron_variant; non_coding_transcript_variant	0.953[CHB]; 1.0[CHD]; 1.0[JPT]
rs3732359	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.954[CHB]; 0.927[CHD]; 0.813[JPT]
rs4688042	intron_variant; non_coding_transcript_variant	0.867[JPT]
rs10934502	intron_variant	0.867[JPT]
rs12630592	intron_variant	0.907[CHB]; 1.0[CHD]; 1.0[JPT]
rs7639388	intron_variant	0.909[JPT]
rs4687893	intron_variant	0.858[CHB]; 1.0[JPT]
rs4261913	intron_variant; non_coding_transcript_variant	0.954[CHB]; 0.928[CHD]; 0.953[JPT]
rs6438553	intron_variant	1.0[CHB]; 1.0[JPT]
rs4687890	intron_variant; upstream_gene_variant	0.907[CHB]; 1.0[JPT]
rs1154595	intron_variant	0.907[CHB]; 1.0[JPT]
rs6795653	intron_variant	0.954[CHB]; 1.0[CHD]; 1.0[JPT]
rs334533	intron_variant	0.862[CHB]; 1.0[CHD]; 1.0[JPT]
rs1574154	intron_variant	0.867[JPT]
rs4688047	intron_variant	0.867[JPT]
rs6808874	intron_variant; non_coding_transcript_variant	0.867[JPT]
rs10934503	intron_variant	0.861[JPT]
rs13321783	intron_variant	0.954[CHB]; 1.0[CHD]; 1.0[JPT]
rs1732170	intron_variant; non_coding_transcript_variant	0.861[CHB]; 0.975[CHD]; 1.0[JPT]
rs4688059	intron_variant; upstream_gene_variant	0.814[JPT]
rs28536662	intron_variant	0.907[CHB]; 1.0[CHD]; 1.0[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
Saus, E.,2010	association analyses with diagnosis:codominant P-value = 0.228, dominant P-value = 0.277, recessive P-value = 0.109, additive P-value = 0.102	No significant association was observed.	Negative