BDgene

SNP Report

Basic Info
Name rs6102917 dbSNP Ensembl
Location chr20:42590779 - 42590779(1)
Variant Alleles C/G
Ancestral Allele C
Minor Allele G
Minor Allele Frequence 0.149161
Functional Annotation intron_variant; NMD_transcript_variant.
Consequence to Transcript intron_variant(ENST00000356100, ENST00000373184, ENST00000373187, ENST00000373190, ENST00000373193, ENST00000373198, ENST00000373201, ENST00000617474); NMD_transcript_variant(ENST00000617474)
No. of Studies 1 (Positive: 0; Negative: 1; Trend: 0)
Source Literature
Overlap with SZ? NO
Overlap with MDD? NO

SNP related studies (count: 1)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Sklar, P.,2011 C/G Primary GWAS P-value(GC)=0.0000388, OR=1.44; replication P-v...... Primary GWAS P-value(GC)=0.0000388, OR=1.44; replication P-value(1-sided)=0.165, OR=1.11; Combined GWAS and replication P-value(GC)=0.0000846, OR=1.31 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)
PTPRT protein tyrosine phosphatase, receptor type, T 20q12-q13 2(0/1/1)

SNPs in LD with rs6102917 (count: 13) View in gBrowse (chr20:42590779..42627137 )
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: 13)


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

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