SNP Report

Basic Info

Name	rs10462020 dbSNP Ensembl
Location	chr1:7820623 - 7820623(1)
Variant Alleles	T/G
Ancestral Allele	T
Minor Allele	G
Minor Allele Frequence	0.120607
Functional Annotation	intron_variant; missense_variant; non_coding_transcript_variant. Polyphen Annotation: benign(ENST00000361923, ENST00000377532, ENST00000613533, ENST00000614998) SIFT Annotation: deleterious(ENST00000361923, ENST00000377532, ENST00000613533, ENST00000614998)
Consequence to Transcript	intron_variant(ENST00000451646); missense_variant(ENST00000361923, ENST00000377532, ENST00000613533, ENST00000614998); non_coding_transcript_variant(ENST00000451646)
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
Mansour, H. A., 2006	T/G		TDT P-value = 0.784 in the samples combined, Pittsburgh Tren...... TDT P-value = 0.784 in the samples combined, Pittsburgh Trends test=0.07 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

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 rs10462020 (count: 4) View in gBrowse (chr1:7792859..7831318 )

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

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

Reference	Statistical Result	Description	Result Category
Mansour, H. A., 2006	TDT P-value = 0.317, Trends test=0.08 for Pittsburgh SZ/SZA		Negative

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