SNP Report

Basic Info

Name	rs10517263 dbSNP Ensembl
Location	chr4:52632502 - 52632502(1)
Variant Alleles	G/C
Ancestral Allele	G
Minor Allele	C
Minor Allele Frequence	0.13778
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000441222, ENST00000451218, ENST00000503060, ENST00000504078, ENST00000506707, ENST00000508499, ENST00000512656, ENST00000514536); NMD_transcript_variant(ENST00000503060, ENST00000512656, ENST00000514536); non_coding_transcript_variant(ENST00000504078, ENST00000506707); upstream_gene_variant(ENST00000502443)
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
Kushima, I.,2010	G/C		Allele-/genotype wise analyses: X² test, allele P...... Allele-/genotype wise analyses: X² test, allele P-value > 0.05; genotype P-value > 0.05 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)
USP46	ubiquitin specific peptidase 46	4q12	1(0/1/0)

SNPs in LD with rs10517263 (count: 20) View in gBrowse (chr4:52549359..52722288 )

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]
rs17051548		0.904[CHB]; 1.0[JPT]
rs7691678	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs10517266	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs11946547		1.0[CHB]; 1.0[JPT]
rs2411261		1.0[CHB]; 1.0[JPT]
rs17051550		0.904[CHB]; 0.808[CHD]; 1.0[JPT]
rs7674000	non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CHB]; 0.927[CHD]; 1.0[JPT]
rs17051667	downstream_gene_variant; upstream_gene_variant	1.0[CHB]
rs17051666	downstream_gene_variant; upstream_gene_variant	1.0[CHB]
rs346928		0.814[CHB]; 0.823[JPT]
rs12500617	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs11939490	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.927[CHD]; 1.0[JPT]
rs7680727	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.927[CHD]; 1.0[JPT]
rs11936731		0.814[CHB]; 1.0[JPT]
rs17051640	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.911[CHB]; 1.0[JPT]
rs17051554		0.904[CHB]; 1.0[JPT]
rs12513215	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.927[CHD]; 1.0[JPT]
rs346927		0.814[CHB]; 0.823[JPT]
rs17051576	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs17051547		0.904[CHB]; 0.808[CHD]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Kushima, I.,2010	Allele-/genotype wise analyses:X² test, allele P-value > 0.05;genotype P-value > 0.05	No significant association was observed.	Negative

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