BDgene

SNP Report

Basic Info
Name rs1042779 dbSNP Ensembl
Location chr3:52786995 - 52786995(1)
Variant Alleles A/G
Ancestral Allele G
Minor Allele G
Minor Allele Frequence 0.42472
Functional Annotation downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant.
Polyphen Annotation: benign(ENST00000273283, ENST00000428133, ENST00000484844, ENST00000537050)
SIFT Annotation: tolerated(ENST00000273283, ENST00000428133, ENST00000484844, ENST00000537050)
Consequence to Transcript downstream_gene_variant(ENST00000478667, ENST00000487686, ENST00000494603); missense_variant(ENST00000273283, ENST00000428133, ENST00000484844, ENST00000537050); NMD_transcript_variant(ENST00000484844); non_coding_transcript_exon_variant(ENST00000628722); non_coding_transcript_variant(ENST00000628722); upstream_gene_variant(ENST00000405128, ENST00000482836, ENST00000494705)
No. of Studies 2 (Positive: 1; Negative: 0; Trend: 1)
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
Kondo, K.,2013 A/G P-value = 0.025,OR= 1.14 P-value = 0.025,OR= 1.14 Significant association was observed. Significant association was observed. Positive
Scott, L. J.,2009 A/G NIMH/Pritzker: OR (95% CI)=1.2(1.04-1.38), P-value = 0.015; ...... NIMH/Pritzker: OR (95% CI)=1.2(1.04-1.38), P-value = 0.015; GSK(reduced sample): OR (95% CI)=1.31(1.11-1.54), P-value = 0.0012; WTCCC: OR (95% CI)=1.16(1.07-1.25), P-value = 0.00012; 3-study meta-analysis: OR (95% CI)=1.19(1.11-1.27), P-value = 0.00000018; Heterogeneity: I2%=0, P-value = 0.4 More... Trend

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
ITIH1 inter-alpha-trypsin inhibitor heavy chain 1 3p21.1 1(1/0/0)

SNPs in LD with rs1042779 (count: 91) View in gBrowse (chr3:52587823..52813585 )
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: 91)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Kondo, K.,2013 P-value = 0.012,OR= 1.16 Significant association was observed. Positive

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