BDgene

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.

Literature-origin SNPs (count: 0)

LD-proxies (count: 4)


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)