SNP Report

Basic Info

Name	rs1701946 dbSNP Ensembl
Location	chr19:51000268 - 51000268(1)
Variant Alleles	T/C/G
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.464856
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000250366, ENST00000544410, ENST00000594211, ENST00000599710); intron_variant(ENST00000291726, ENST00000320838, ENST00000347619, ENST00000391806, ENST00000593490, ENST00000594512, ENST00000594669, ENST00000595238, ENST00000599166, ENST00000600767); NMD_transcript_variant(ENST00000594669, ENST00000599166); non_coding_transcript_variant(ENST00000594512); upstream_gene_variant(ENST00000594914, ENST00000598195)
No. of Studies	1 (Positive: 1; Negative: 0; 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
Izumi, A., 2008	g.IVS3-10A>G		Genotype frequency (df=2) X²=6.3 , P value=0.042 ...... Genotype frequency (df=2) X²=6.3 , P value=0.042 . Allele frequency (df=1) X²=5.56 , P value=0.018 in Patients with BD vs controls. More...	A significant allelic association was found between SNP and ...... A significant allelic association was found between SNP and bipolar disorder More...	Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
KLK9	kallikrein-related peptidase 9	19q13.33	Mapped by Literature SNP
KLK8	kallikrein-related peptidase 8	19q13	1(1/0/0)

SNPs in LD with rs1701946 (count: 11) View in gBrowse (chr19:50986200..51000268 )

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]
rs268894	intron_variant; non_coding_transcript_variant	0.862[CHB]; 1.0[JPT]
rs1654520	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.857[CHB]; 1.0[JPT]
rs268899	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.857[CHB]; 1.0[JPT]
rs1722560	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.953[CHB]; 1.0[JPT]
rs268897	intron_variant; non_coding_transcript_variant	0.86[CHB]; 1.0[JPT]
rs1654521	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.862[CHB]; 1.0[JPT]
rs1722545	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.862[CHB]; 1.0[JPT]
rs1722546	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.811[CHB]; 1.0[JPT]
rs2659071	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.955[CHB]; 1.0[JPT]
rs1701948	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.811[CHB]; 1.0[JPT]
rs268898	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.862[CHB]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Izumi, A., 2008	Genotype frequency (df=2) X²=3.26, P value=0.20. Allele frequency (df=1) X²=2.36, P value=0.12 in Patients with SZ vs controls.	There was no significant difference in genotype or allele distribution for any SNP between patients and controls for schizophrenia or major depression.	Negative

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

Reference	Statistical Result	Description	Result Category
Izumi, A., 2008	Genotype frequency (df=2) X²=0.33, P value=0.85 . Allele frequency (df=1) X²=0.21, P value=0.65 in Patients with MD vs controls.	There was no significant difference in genotype or allele distribution for any SNP between patients and controls for schizophrenia or major depression.	Negative