SNP Report

Basic Info

Name	rs2400546 dbSNP Ensembl
Location	chr12:79670586 - 79670586(1)
Variant Alleles	A/T
Ancestral Allele	T
Minor Allele	T
Minor Allele Frequence	0.299521
Functional Annotation	intron_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000328827, ENST00000547571, ENST00000550006, ENST00000551712); non_coding_transcript_variant(ENST00000547571, ENST00000550006)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Kishi, T., 2008 (a)	A > T		Hardy-Weinberg equilibrium P value=0.403, genotypic P value=...... Hardy-Weinberg equilibrium P value=0.403, genotypic P value=0.953, allelic P value=0.717 for bipolor disorder compared with controls. More...		Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
PAWR	PRKC, apoptosis, WT1, regulator	12q21.2	1(0/1/0)

SNPs in LD with rs2400546 (count: 65) View in gBrowse (chr12:79481238..79714636 )

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: 65)

rs_ID	Functional Annotation	r²[population]
rs10861993	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs8176805	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.879[CHB]; 1.0[JPT]
rs10862007	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs10778685	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs3842842	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.904[JPT]
rs11503488	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7134813	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7969760		1.0[CHB]; 1.0[JPT]
rs2463168	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs711159	intron_variant; non_coding_transcript_variant	0.81[CHB]
rs7134679	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs12306147	downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs2491341	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs3995243	intron_variant; non_coding_transcript_variant	0.873[CHB]
rs11114162	upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs10778686	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.877[JPT]
rs2463108	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs6539469	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7975021		1.0[CHB]; 1.0[JPT]
rs7297309		0.936[CHB]; 0.877[JPT]
rs4441080	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs6539468		1.0[CHB]; 1.0[JPT]
rs12308122	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs12230772		1.0[CHB]; 1.0[JPT]
rs12316573	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs11114218	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs1880883	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs2694831	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs9651966	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs10861992	downstream_gene_variant	0.878[CHB]; 1.0[JPT]
rs11114183	downstream_gene_variant	1.0[JPT]
rs2430866	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs11114128	intron_variant; non_coding_transcript_variant	0.874[CHB]
rs2049589	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs10861991	upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs11114201	intron_variant; non_coding_transcript_variant	0.919[CHB]
rs4083220	intron_variant; non_coding_transcript_variant	0.873[CHB]
rs11114173	downstream_gene_variant	0.879[CHB]
rs2808356	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs11114185	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs10778678	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs7305134	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs10506816		1.0[CHB]; 1.0[JPT]
rs1880884	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs10778677	non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7307647	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7979987	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7955388	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs11114178	downstream_gene_variant	0.896[JPT]
rs11114170	downstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs2177973	intron_variant; non_coding_transcript_variant	0.937[CHB]
rs7953683	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs8176857	intron_variant; non_coding_transcript_variant	0.936[CHB]; 0.888[JPT]
rs7294911	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs10778679	non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs6539471	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs10778681	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs8176875	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7300145	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs8176914	3_prime_UTR_variant; downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7967604		1.0[CHB]; 1.0[JPT]
rs7306065	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7138068	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.874[CHB]
rs2049590	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs10778683	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Kishi, T., 2008 (a)	Hardy-Weinberg equilibrium P value=0.106, genotypic P value=0.786, allelic P value=0.474 for schizophrenia compared with controls.	No association was detected with schizophrenia or MDD in allele/genotype-wise analyses.	Negative

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

Reference	Statistical Result	Description	Result Category
Kishi, T., 2008 (a)	Hardy-Weinberg equilibrium P value=0.408, genotypic P value=0.453, allelic P value=0.656 for MDD compared with controls.	No association was detected with schizophrenia or MDD in allele/genotype-wise analyses.	Negative