SNP Report

Basic Info

Name	rs7178572 dbSNP Ensembl
Location	chr15:77454848 - 77454848(1)
Variant Alleles	A/G
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.474441
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000336216, ENST00000381714, ENST00000558176, ENST00000558651, ENST00000559035, ENST00000559099, ENST00000560498, ENST00000560986); NMD_transcript_variant(ENST00000559035); non_coding_transcript_variant(ENST00000560986); upstream_gene_variant(ENST00000560867)
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	G/A		P-value=0.0043, Pcorrected=0.14, OR=0.82 for BD in screening...... P-value=0.0043, Pcorrected=0.14, OR=0.82 for BD in screening stage, P-value=0.56, OR=0.97 for replication. More...	The BD associations exhibited nominal significance for SNPs ...... The BD associations exhibited nominal significance for SNPs in HMG20A (rs7178572, Puncorrected=0.0043). More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
HMG20A	high mobility group 20A	15q24	1(1/0/0)

SNPs in LD with rs7178572 (count: 49) View in gBrowse (chr15:77292156..77556464 )

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: 49)

rs_ID	Functional Annotation	r²[population]
rs11636554	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.908[JPT]
rs4886875		0.905[JPT]
rs1005752	non_coding_transcript_exon_variant; non_coding_transcript_variant	0.952[CHB]; 0.908[JPT]
rs8024485	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.906[JPT]
rs965480	downstream_gene_variant; upstream_gene_variant	0.952[CHB]; 1.0[JPT]
rs12901503	intron_variant; non_coding_transcript_variant	0.948[CHB]; 0.908[JPT]
rs6495237	intron_variant; non_coding_transcript_variant	0.95[CHB]; 0.906[JPT]
rs1565756	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.908[JPT]
rs12900004		0.858[JPT]
rs11854328		0.84[JPT]
rs869301	downstream_gene_variant	0.905[JPT]
rs7166927	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.975[CHD]; 0.906[JPT]
rs6495240	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs4886869		1.0[CHB]; 1.0[JPT]
rs4886876		0.902[JPT]
rs907388	downstream_gene_variant	0.81[CHB]; 0.953[JPT]
rs34591043	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 0.908[JPT]
rs11855188		0.864[JPT]
rs11072653	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.906[JPT]
rs7167794	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.904[JPT]
rs11857294	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.908[JPT]
rs1191196	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.908[JPT]
rs2175941	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.906[JPT]
rs1473922	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.908[JPT]
rs4886866	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.908[JPT]
rs11857450		1.0[CHB]; 0.952[CHD]; 1.0[JPT]
rs7171448		0.846[JPT]
rs7177055		0.865[JPT]
rs12914345	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.908[JPT]
rs12911371	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.899[JPT]
rs12905951	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.904[JPT]
rs4886515	intron_variant; non_coding_transcript_variant	1.0[CHB]
rs1602925	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.908[JPT]
rs8034133	downstream_gene_variant; intron_variant	1.0[CHB]; 1.0[JPT]
rs11858641	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.908[JPT]
rs11632966	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.908[JPT]
rs12901130		1.0[JPT]
rs1565757	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.908[JPT]
rs4886862	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.976[CHD]; 0.908[JPT]
rs11857860		0.905[JPT]
rs2055901	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs12324627	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs7170877		0.844[CHB]; 0.946[JPT]
rs11633054	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs4886877		0.905[JPT]
rs12907746		0.858[JPT]
rs12910361	downstream_gene_variant; upstream_gene_variant	0.945[CHB]; 1.0[JPT]
rs1022172		1.0[CHB]; 1.0[JPT]
rs1493700	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.908[JPT]

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

Reference	Statistical Result	Description	Result Category
Kajio, Y., 2014	P-value=0.25, Pcorrected=1, OR=0.93 for SZ in screening stage, P-value=0.28, OR=1.05 for replication.	No association was found for SZ.	Negative

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