SNP Report

Basic Info

Name	rs1539628 dbSNP Ensembl
Location	chr10:22638943 - 22638943(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	G
Minor Allele Frequence	0.272764
Functional Annotation	downstream_gene_variant; intron_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000605011); intron_variant(ENST00000376573, ENST00000545335)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Jamra, R. A., 2006 (a)	A/G		ARMITAGE P-value = 0.198 for BPAD ARMITAGE P-value = 0.198 for BPAD	In the single marker analysis, none of the analyzed variants...... In the single marker analysis, none of the analyzed variants revealed significant association to disease status, neither for schizophrenia nor for BPAD. More...	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
PIP4K2A	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	10p12.2	4(1/3/0)

SNPs in LD with rs1539628 (count: 10) View in gBrowse (chr10:22638943..22662938 )

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]
rs1778338	intron_variant; non_coding_transcript_variant	0.81[TSI]
rs2154053	intron_variant; non_coding_transcript_variant	0.81[TSI]
rs1171492	intron_variant; non_coding_transcript_variant	0.81[TSI]
rs943196	downstream_gene_variant; intron_variant	0.81[TSI]
rs2559534	downstream_gene_variant; intron_variant	0.81[TSI]
rs1171506	intron_variant; non_coding_transcript_variant	0.834[TSI]
rs1750775	intron_variant; non_coding_transcript_variant	0.81[TSI]
rs1778335	intron_variant; non_coding_transcript_variant	0.81[TSI]
rs1614387	intron_variant; non_coding_transcript_variant	0.804[TSI]
rs1750747	downstream_gene_variant; intron_variant	0.81[TSI]

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

Reference	Statistical Result	Description	Result Category
Jamra, R. A., 2006 (a)	ARMITAGE P-value = 0.544 for Schizophrenia	In the single marker analysis, none of the analyzed variants revealed significant association to disease status, neither for schizophrenia nor for BPAD.	Negative

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