SNP Report

Basic Info

Name	rs10462021 dbSNP Ensembl
Location	chr1:7837073 - 7837073(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.121006
Functional Annotation	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant. Polyphen Annotation: benign(ENST00000361923, ENST00000377532, ENST00000613533, ENST00000614998) SIFT Annotation: tolerated(ENST00000361923, ENST00000377532, ENST00000613533, ENST00000614998)
Consequence to Transcript	missense_variant(ENST00000361923, ENST00000377532, ENST00000613533, ENST00000614998); non_coding_transcript_exon_variant(ENST00000494684); non_coding_transcript_variant(ENST00000494684)
No. of Studies	2 (Positive: 0; Negative: 2; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Mansour, H. A., 2006	C/T		TDT P-value = 0.68 in the samples combined, Pittsburgh Trend...... TDT P-value = 0.68 in the samples combined, Pittsburgh Trends test=0.281 for BDI More...	The loci tested did not show significant differences between...... The loci tested did not show significant differences between sites in the transmission rate. More...	Negative
Mansour, H. A.,2009			Single SNP-based analyses: Trends test P-value = 0.334 in BP...... Single SNP-based analyses: Trends test P-value = 0.334 in BPI More...	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)
PER3	period circadian clock 3	1p36.23	7(3/4/0)

SNPs in LD with rs10462021 (count: 4) View in gBrowse (chr1:7792859..7837073 )

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]
rs12130462	intron_variant; upstream_gene_variant	1.0[CEU]
rs875994	downstream_gene_variant; intron_variant	0.82[CEU]; 0.871[TSI]
rs17374439	intron_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs10864316	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Mansour, H. A.,2009	Single SNP-based analyses:Trends test P-value = 0.036 in SZ	Significant association was observed	Positive
Mansour, H. A., 2006	TDT P-value = 0.485, Trends test=0.913 for Pittsburgh SZ/SZA		Negative

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