BDgene

SNP Report

Basic Info
Name rs420259 dbSNP Ensembl
Location chr16:23622705 - 23622705(1)
Variant Alleles A/G
Ancestral Allele G
Minor Allele G
Minor Allele Frequence 0.357428
Functional Annotation downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript downstream_gene_variant(ENST00000565038); intron_variant(ENST00000261584, ENST00000561764, ENST00000568219, LRG_308t1); non_coding_transcript_variant(ENST00000561764); upstream_gene_variant(ENST00000566069)
No. of Studies 5 (Positive: 3; Negative: 2; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? NO

SNP related studies (count: 5)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Tesli, M.,2010 G/A CMH test: P-value = 0.025, OR (95% CI)=0.84(0.72-0.98) for B...... CMH test: P-value = 0.025, OR (95% CI)=0.84(0.72-0.98) for BD. More... Significant association was found in BD. Significant association was found in BD. Positive
Yosifova, A.,2009 A/G Allelic association: P-value = 0.052 Allelic association: P-value = 0.052 No significant association was observed No significant association was observed Negative
Ollila, H. M.,2009 A/G FBAT: P-value = 0.378765 FBAT: P-value = 0.378765 No significant association was observed No significant association was observed Negative
Jiang, Y.,2011 Non-weighted test under H0: P-value(additive)=0.000219, P-va...... Non-weighted test under H0: P-value(additive)=0.000219, P-value(dominant)=0.0966, P-value(recessive)=0.00000000851; weighted test under H'0: P-value(additive)=0.000647, P-value(dominant)=0.12, P-value(recessive)=0.0000000659; logistic regression: P-value(additive)=0.000426, P-value(dominant)=0.151, P-value(recessive)=0.00000000333 More... Significant associations were found . Significant associations were found . Positive
The Wellcome Trust Case Control Consortium, 2007 A/G A Genotypic P-value = 6.29E-08; Heterozygote OR (95%CI)=2.08(...... Genotypic P-value = 6.29E-08; Heterozygote OR (95%CI)=2.08(1.60-2.71); Homozygote OR (95%CI)=2.07 (1.6-2.69) More... The strongest signal in BD was with rs420259 at chromosome 1...... The strongest signal in BD was with rs420259 at chromosome 16p12 and the best-fitting genetic model was recessive, but was not additionally supported by the expanded reference group analysis. More... Positive

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
PALB2 partner and localizer of BRCA2 16p12.1 5(2/2/1)

SNPs in LD with rs420259 (count: 1) View in gBrowse (chr16:23622705..23629146 )
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: 1)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Tesli, M.,2010 CMH test:P-value = 0.54, OR (95% CI)=1.04(0.91-1.20) for SCZ. No significant association was observed. Negative

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