SNP Report

Basic Info

Name	rs6001093 dbSNP Ensembl
Location	chr22:38305388 - 38305388(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	C
Minor Allele Frequence	0.302516
Functional Annotation	intron_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000359867, ENST00000396832, ENST00000400206, ENST00000403904, ENST00000405675, ENST00000413574, ENST00000430335); upstream_gene_variant(ENST00000431611, ENST00000451964, ENST00000612795)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Matsunaga, S.,2012	C/T		Chi square test:MAF = 0.1,P-value = 0.12,OR = 1.16 Chi square test:MAF = 0.1,P-value = 0.12,OR = 1.16	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)
CSNK1E	casein kinase 1, epsilon	22q13.1	5(1/3/1)

SNPs in LD with rs6001093 (count: 3) View in gBrowse (chr22:38299094..38307584 )

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]
rs135756	intron_variant; upstream_gene_variant	0.823[JPT]
rs1534891	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.823[JPT]
rs5750581	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.842[CHB]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Matsunaga, S.,2012	Chi square test:MAF = 0.08,P-value = 0.18,OR = 0.86	No significant association was observed.	Negative

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

Reference	Statistical Result	Description	Result Category
Matsunaga, S.,2012	Chi square test:MAF = 0.09,P-value = 0.92,OR = 0.99	No significant association was observed.	Negative