BDgene

SNP Report

Basic Info
Name rs2413338 dbSNP Ensembl
Location chr22:35267530 - 35267530(1)
Variant Alleles C/T
Ancestral Allele C
Minor Allele T
Minor Allele Frequence 0.438698
Functional Annotation downstream_gene_variant; intron_variant; NMD_transcript_variant.
Consequence to Transcript downstream_gene_variant(ENST00000420166, ENST00000455359, ENST00000464480, ENST00000498325); intron_variant(ENST00000216106, ENST00000418170); NMD_transcript_variant(ENST00000418170)
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/T Family-based P-value = 0.046 for all BPAD subjects, family-b...... Family-based P-value = 0.046 for all BPAD subjects, family-based P-value = 0.01 for BPAD subjects with psychotic symptoms, family-based P-value = 0.045 (3-marker sliding window with indicated marker first of the three), family-based P-value = 0.012 (3-marker sliding window with indicated marker first of the three using only those BPAD subjects with psychotic symptoms).Case-control P-value = 0.15 for all BPAD subjects, case-control P-value = 0.12 for BPAD subjects with psychotic symptoms, case-control P-value = 0.35 (3-marker sliding window with indicated marker first of the three), case-control P-value = 0.27 (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)
HMGXB4 HMG box domain containing 4 22q13 1(1/0/0)

SNPs in LD with rs2413338 (count: 46) View in gBrowse (chr22:35250868..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: 46)


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