SNP Report

Basic Info

Name	rs3890379 dbSNP Ensembl
Location	chr22:38296374 - 38296374(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.0990415
Functional Annotation	3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant.
Consequence to Transcript	3_prime_UTR_variant(ENST00000405675, ENST00000413574); downstream_gene_variant(ENST00000430335, ENST00000442216, ENST00000451964, ENST00000498529, ENST00000612795); intron_variant(ENST00000359867, ENST00000396832, ENST00000400206, ENST00000403904, ENST00000431611, ENST00000431632); NMD_transcript_variant(ENST00000431611); upstream_gene_variant(ENST00000366216, ENST00000494610, ENST00000495232)
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	G/A		Chi square test:MAF = 0.16,P-value = 0.052,OR = 1.17 Chi square test:MAF = 0.16,P-value = 0.052,OR = 1.17	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 rs3890379 (count: 3) View in gBrowse (chr22:38296374..38312601 )

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]
rs7284708	intron_variant; upstream_gene_variant	0.941[CHD]
rs867198	intron_variant	0.941[CHD]; 0.846[JPT]
rs1005473	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	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 = 0.15,P-value = 0.49,OR = 1.06	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 = 0.14,P-value = 0.69,OR = 0.96	No significant association was observed.	Negative