BDgene

SNP Report

Basic Info
Name rs2289247 dbSNP Ensembl
Location chr3:52693241 - 52693241(1)
Variant Alleles G/A
Ancestral Allele A
Minor Allele A
Minor Allele Frequence 0.445088
Functional Annotation downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant.
Polyphen Annotation: benign(ENST00000394799, ENST00000418458)
SIFT Annotation: tolerated(ENST00000394799, ENST00000418458)
Consequence to Transcript downstream_gene_variant(ENST00000266014, ENST00000391150, ENST00000391191, ENST00000394783, ENST00000410413, ENST00000459623, ENST00000463827, ENST00000468146, ENST00000478968, ENST00000479230, ENST00000479553, ENST00000480080, ENST00000481643, ENST00000484022, ENST00000484163, ENST00000485899, ENST00000487642, ENST00000489119, ENST00000491606, ENST00000492349, ENST00000497436, ENST00000497953, ENST00000516978, ENST00000630615); missense_variant(ENST00000394799, ENST00000418458); non_coding_transcript_exon_variant(ENST00000496254, ENST00000497356); non_coding_transcript_variant(ENST00000496254, ENST00000497356)
No. of Studies 1 (Positive: 1; Negative: 0; Trend: 0)
Source Literature
Overlap with SZ? NO
Overlap with MDD? YES

SNP related studies (count: 1)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
McMahon, F. J., 2010 There was strong linkage disequilibrium (LD) between rs22512...... There was strong linkage disequilibrium (LD) between rs2251219 and rs2289247, which is significant in the GAIN-MDD sample. More... Positive

SNP related genes (count: 5)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
GLT8D1 glycosyltransferase 8 domain containing 1 3p21.1 1(1/0/0)
SNORD19 small nucleolar RNA, C/D box 19 3p21.1 Mapped by Literature SNP
SNORD69 small nucleolar RNA, C/D box 69 3p21.1 Mapped by Literature SNP
GNL3 guanine nucleotide binding protein-like 3 (nucleolar) 3p21.1 2(2/0/0)
SNORD19B small nucleolar RNA, C/D box 19B 3p21.1 Mapped by Literature SNP

SNPs in LD with rs2289247 (count: 90) View in gBrowse (chr3:52526005..52789110 )
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: 90)


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

Overlap with MDD from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
McMahon, F. J., 2010 P-value = 8.96E-7 for a meta-analysis in the GAIN-MDD sample. It is significant in the GAIN-MDD sample. Positive

Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback Acknowledgements
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Last update: March 31, 2016