SNP Report

Basic Info

Name	rs4812829 dbSNP Ensembl
Location	chr20:44360627 - 44360627(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.255391
Functional Annotation	intron_variant.
Consequence to Transcript	intron_variant(ENST00000316673, ENST00000457232, ENST00000609262, ENST00000609795, ENST00000619550, LRG_483t1, LRG_483t3)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Kajio, Y., 2014	A/G		P-value=0.0082, Pcorrected=0.26, OR=0.84 for BD in screening...... P-value=0.0082, Pcorrected=0.26, OR=0.84 for BD in screening stage, P-value=0.49, OR=1.03 for replication. More...	SNPs in HNF4A (rs4812829, Puncorrected=0.0082) showed the op...... SNPs in HNF4A (rs4812829, Puncorrected=0.0082) showed the opposite direction of effect in the BD associations. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HNF4A	hepatocyte nuclear factor 4, alpha	20q13.12	1(1/0/0)

SNPs in LD with rs4812829 (count: 5) View in gBrowse (chr20:44351775..44361137 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs2144908	intron_variant; upstream_gene_variant	0.909[CHB]; 1.0[CHD]; 0.952[JPT]
rs1884614	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.953[CHB]; 0.954[CHD]; 0.952[JPT]
rs6031544	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.977[CHD]; 0.952[JPT]
rs1884613	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.95[JPT]
rs16988991	intron_variant	1.0[CHB]; 1.0[CHD]; 0.952[JPT]

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Kajio, Y., 2014	P-value=0.281, Pcorrected=1.0, OR=0.93 for SZ in screening stage, P-value=0.49, OR=1.03 for replication.	No association was found for SZ.	Negative

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