SNP Report

Basic Info

Name	rs2279287 dbSNP Ensembl
Location	chr11:13276938 - 13276938(1)
Variant Alleles	T/C
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.425519
Functional Annotation	5_prime_UTR_variant; upstream_gene_variant.
Consequence to Transcript	5_prime_UTR_variant(ENST00000529050, ENST00000534544); upstream_gene_variant(ENST00000389707, ENST00000401424, ENST00000403290, ENST00000403510, ENST00000480685, ENST00000482049, ENST00000527998, ENST00000529388, ENST00000529825, ENST00000530357, ENST00000533520)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Soria, V.,2010			X²-tests: allele P-value > 0.05, genotype P-value...... X²-tests: allele P-value > 0.05, genotype P-value > 0.05 in all model More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Mansour, H. A., 2006	A/G		TDT P-value = 0.322, X²=3.92, df=1 in the samples...... TDT P-value = 0.322, X²=3.92, df=1 in the samples combined, Pittsburgh Trends test=0.056 for BDI More...	We observed significant transmission bias when we analyzed t...... We observed significant transmission bias when we analyzed transmission distortion of the bipolar samples jointly More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
ARNTL	aryl hydrocarbon receptor nuclear translocator-like	11p15	7(5/2/0)

SNPs in LD with rs2279287 (count: 38) View in gBrowse (chr11:13248001..13302983 )

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: 38)

rs_ID	Functional Annotation	r²[population]
rs10832012	upstream_gene_variant	0.864[CEU]; 0.86[TSI]
rs11022733		0.864[CEU]
rs10832021	intron_variant; non_coding_transcript_variant	0.859[TSI]
rs4146388	intron_variant; non_coding_transcript_variant	0.864[CEU]; 0.803[TSI]
rs986720		0.864[CEU]
rs2403662	intron_variant; non_coding_transcript_variant	0.953[CEU]
rs7109016	upstream_gene_variant	0.953[CEU]; 1.0[TSI]
rs6486120	intron_variant; non_coding_transcript_variant	0.857[TSI]
rs11022755	intron_variant; non_coding_transcript_variant	0.905[CEU]
rs986721		0.864[CEU]
rs2279284	intron_variant; upstream_gene_variant	0.908[CEU]; 0.86[TSI]
rs7951393	intron_variant; non_coding_transcript_variant	0.834[TSI]
rs10766065		0.864[CEU]
rs900147	upstream_gene_variant	0.947[CEU]
rs7114573	intron_variant; non_coding_transcript_variant	0.859[TSI]
rs900145	upstream_gene_variant	0.903[CEU]; 1.0[TSI]
rs4414197	intron_variant; non_coding_transcript_variant	0.953[CEU]; 0.942[TSI]
rs12290622	intron_variant; non_coding_transcript_variant	0.953[CEU]; 0.942[TSI]
rs4757138	upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs11022754	intron_variant; non_coding_transcript_variant	0.864[CEU]
rs4757141	intron_variant; non_coding_transcript_variant	0.864[CEU]; 0.83[TSI]
rs998089		0.864[CEU]; 0.86[TSI]
rs11022738		0.864[CEU]; 0.834[TSI]
rs11022742	upstream_gene_variant	0.908[CEU]; 0.86[TSI]
rs6486116	intron_variant; non_coding_transcript_variant	0.859[TSI]
rs11022753	intron_variant; non_coding_transcript_variant	0.864[CEU]; 0.803[TSI]
rs11022750	intron_variant; non_coding_transcript_variant	0.864[CEU]; 0.83[TSI]
rs747601		0.864[CEU]
rs10766064		0.821[CEU]
rs11605518		0.864[CEU]
rs1481880		0.864[CEU]
rs1481891	intron_variant; non_coding_transcript_variant	0.953[CEU]
rs10832007		0.864[CEU]
rs2279285	intron_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs10766066		0.864[CEU]
rs2279286	5_prime_UTR_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs2403661		0.953[CEU]; 0.971[TSI]
rs11022756	intron_variant; non_coding_transcript_variant	0.953[CEU]

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

Reference	Statistical Result	Description	Result Category
Mansour, H. A., 2006	TDT P-value = 0.348, Trends test=0.173 for Pittsburgh SZ/SZA		Negative

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

Reference	Statistical Result	Description	Result Category
Soria, V.,2010	X²-tests:allele P-value = 0.178, Model Dominant, genotype P-value = 0.022, OR(95%CI)=0.71 (0.53-0.95)	Significant association was found.	Positive