SNP Report

Basic Info

Name	rs2702009 dbSNP Ensembl
Location	chr11:125494945 - 125494945(1)
Variant Alleles	C/A/T
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.326278
Functional Annotation	intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000278919, ENST00000366139, ENST00000392709, ENST00000524435, ENST00000527534, ENST00000532981); non_coding_transcript_variant(ENST00000392709, ENST00000532981); upstream_gene_variant(ENST00000527818)
No. of Studies	2 (Positive: 0; Negative: 2; Trend: 0)
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
Hodgkinson, C. A., 2007	C/T		Allelic P-value = 0.485, genotypic P-value = 0.779 in Cauc...... Allelic P-value = 0.485, genotypic P-value = 0.779 in Caucasians. More...	No association to bipolar disorder was found for any of the ...... No association to bipolar disorder was found for any of the nine markers typed in these populations at the allelic or the genotypic level. More...	Negative
Yamada, K.,2004	A/G		Association analysis: Fisher's exact test, allele P-value = ...... Association analysis: Fisher's exact test, allele P-value = 0.491, genotype P-value = 0.819 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
FEZ1	fasciculation and elongation protein zeta 1 (zygin I)	11q24.2	2(0/2/0)

SNPs in LD with rs2702009 (count: 28) View in gBrowse (chr11:125428235..125590585 )

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: 28)

rs_ID	Functional Annotation	r²[population]
rs11220121		1.0[CHB]; 1.0[JPT]
rs6590145	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.83[CHB]; 0.897[JPT]
rs11220081	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.83[CHB]; 0.897[JPT]
rs558816		0.941[CEU]; 1.0[CHB]; 1.0[JPT]
rs11220069	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.83[CHB]; 0.842[JPT]
rs7101969	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.943[CHB]; 0.946[JPT]
rs4627097	3_prime_UTR_variant; downstream_gene_variant; intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_variant; splice_region_variant; synonymous_variant	0.88[CHB]; 0.855[CHD]; 0.947[JPT]
rs7117500	downstream_gene_variant	1.0[CHB]; 0.971[CHD]; 1.0[JPT]
rs7111332	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.943[CHB]; 0.942[CHD]; 0.947[JPT]
rs7128228	downstream_gene_variant	0.83[CHB]; 0.831[CHD]; 0.842[JPT]
rs11220110		1.0[CHB]; 0.948[JPT]
rs3740894	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.83[CHB]; 0.831[CHD]; 0.842[JPT]
rs7112666	downstream_gene_variant	0.83[CHB]; 0.828[CHD]; 0.842[JPT]
rs7945490	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.943[CHB]; 0.943[CHD]; 0.947[JPT]
rs7930295	downstream_gene_variant	0.83[CHB]; 0.831[CHD]; 0.897[JPT]
rs1783926	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 0.971[CHD]; 1.0[JPT]
rs7121855		1.0[CHB]; 0.971[CHD]; 1.0[JPT]
rs2702013		0.941[CEU]; 1.0[TSI]; 1.0[CHB]; 0.971[CHD]; 1.0[JPT]
rs3740893	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.83[CHB]; 0.831[CHD]; 0.84[JPT]
rs515735		0.941[CEU]; 1.0[CHB]; 1.0[JPT]
rs1002777	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.943[CHB]; 0.886[CHD]; 0.947[JPT]
rs10893398		1.0[CHB]; 0.944[CHD]; 1.0[JPT]
rs2845835		0.941[CEU]; 1.0[TSI]; 1.0[CHB]; 0.971[CHD]; 1.0[JPT]
rs1284352	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; splice_region_variant; upstream_gene_variant	0.943[CHB]; 0.888[CHD]; 0.947[JPT]
rs12788600		1.0[CHB]; 1.0[JPT]
rs7936104		1.0[CHB]; 0.971[CHD]; 1.0[JPT]
rs6590146	intron_variant; non_coding_transcript_variant	1.0[CHB]; 0.971[CHD]; 0.947[JPT]
rs7125670		1.0[CHB]; 1.0[JPT]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Hodgkinson, C. A., 2007	Allelic P-value = 0.994, genotypic P-value = 0.900 in Caucasians. Allelic P-value = 0.962, genotypic P-value = 0.363 in African Americans.	No association to schizophrenia was found for any of the nine markers typed in these populations at the allelic or the genotypic level.	Negative
Yamada, K.,2004	Association analysis:Fisher's exact test, allele P-value = 1, genotype P-value = 0.243	No significant association was observed in SZ.	Negative

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