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)

rs_ID	Literature-origin SNPs with LD	Functional Annotation	r²[population]
rs249954		intron_variant; NMD_transcript_variant	0.825[CEU]; 0.937[TSI]

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)