BDgene

SNP Report

Basic Info
Name rs138773 dbSNP Ensembl
Location chr22:35309949 - 35309949(1)
Variant Alleles G/C
Ancestral Allele G
Minor Allele C
Minor Allele Frequence 0.451478
Functional Annotation intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript intron_variant(ENST00000382034, ENST00000395736, ENST00000404284, ENST00000411850, ENST00000424387, ENST00000425375, ENST00000439512, ENST00000447733, ENST00000449058, ENST00000449508, ENST00000456128, ENST00000465529, ENST00000487670, ENST00000608674, ENST00000608749); NMD_transcript_variant(ENST00000395736, ENST00000404284, ENST00000424387, ENST00000439512, ENST00000449508); non_coding_transcript_variant(ENST00000465529, ENST00000487670); upstream_gene_variant(ENST00000443206)
No. of Studies 1 (Positive: 1; Negative: 0; 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
Potash, J. B., 2008 C/G Family-based P-value = 0.04 for all BPAD subjects, family-ba...... Family-based P-value = 0.04 for all BPAD subjects, family-based P-value = 0.009 for BPAD subjects with psychotic symptoms, family-based P-value = 0.03 (3-marker sliding window with indicated marker first of the three), family-based P-value = 0.0076 (3-marker sliding window with indicated marker first of the three using only those BPAD subjects with psychotic symptoms).Case-control P-value = 0.18 for all BPAD subjects, case-control P-value = 0.19 for BPAD subjects with psychotic symptoms, case-control P-value = 0.064 (3-marker sliding window with indicated marker first of the three), case-control P-value = 0.15 (3-marker sliding window with indicated marker first of the three using only those BPAD subjects with psychotic symptoms). More... The strongest signal in the family-based analysis emerged fr...... The strongest signal in the family-based analysis emerged from the 11 SNP HMG2L1/TOM1 haploblock. More... Positive

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
TOM1 target of myb1 (chicken) 22q13.1 1(1/0/0)

SNPs in LD with rs138773 (count: 52) View in gBrowse (chr22:35244950..35316184 )
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: 52)


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

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

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