SNP Report

Basic Info

Name	rs2709722 dbSNP Ensembl
Location	chr7:20828189 - 20828189(1)
Variant Alleles	C/T
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.48722
Functional Annotation	downstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000405810)
No. of Studies	2 (Positive: 1; Negative: 0; Trend: 1)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Lee, M. T.,2011	C/T		Genome-wide association: in joint analysis, TT&CT vs. CC, P-...... Genome-wide association: in joint analysis, TT&CT vs. CC, P-value = 4.65E-06; genotype , P-value = 6.59E-05 More...	Suggestive association was found. Suggestive association was found.	Trend
Kondo, K.,2013	T/C		P-value = 0.0063,OR= 0.838;P-value = 0.023,P-vorrection = 0....... P-value = 0.0063,OR= 0.838;P-value = 0.023,P-vorrection = 0.046,OR = 0.88 for replication. More...	Significant association was observed. Significant association was observed.	Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
SP8	Sp8 transcription factor	7p21.2	3(2/0/1)
RPL23P8	ribosomal protein L23 pseudogene 8	7p15.3	Mapped by Literature SNP

SNPs in LD with rs2709722 (count: 25) View in gBrowse (chr7:20800755..20858290 )

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: 25)

rs_ID	Functional Annotation	r²[population]
rs2529761	upstream_gene_variant	0.953[CHB]; 1.0[JPT]
rs974213	intron_variant; non_coding_transcript_variant	0.885[JPT]
rs2709744		0.948[CHB]; 1.0[JPT]
rs2058075	intron_variant; non_coding_transcript_variant	0.881[JPT]
rs4721954	upstream_gene_variant	0.945[CHB]; 1.0[JPT]
rs2709741	upstream_gene_variant	0.953[CHB]; 1.0[JPT]
rs10276458	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.833[JPT]
rs10269228	intron_variant; non_coding_transcript_variant	0.885[JPT]
rs1981619	intron_variant; non_coding_transcript_variant	0.832[JPT]
rs12535135	intron_variant; non_coding_transcript_variant	0.884[JPT]
rs1981618	intron_variant; non_coding_transcript_variant	0.821[JPT]
rs2709746		0.858[CHB]
rs740399	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.832[JPT]
rs4721955	intron_variant; non_coding_transcript_variant	0.877[JPT]
rs10274248	upstream_gene_variant	0.948[CHB]; 1.0[JPT]
rs2709721	upstream_gene_variant	0.929[CHD]; 0.887[JPT]
rs7779724	intron_variant; non_coding_transcript_variant	0.817[JPT]
rs2108520		0.858[CHB]; 0.904[CHD]; 0.944[JPT]
rs4719631	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.885[JPT]
rs6965781	upstream_gene_variant	0.941[JPT]
rs12537837	intron_variant; non_coding_transcript_variant	0.942[JPT]
rs2709716	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.832[JPT]
rs974212	intron_variant; non_coding_transcript_variant	0.885[JPT]
rs6960772	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.832[JPT]
rs204575	intron_variant; non_coding_transcript_variant	0.884[JPT]

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

Reference	Statistical Result	Description	Result Category
Kondo, K.,2013	P-value = 0.0024,OR= 0.82;P-value = 0.049,P-vorrection = 0.098,OR = 0.922 for replication.	Significant association was observed.	Positive

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