SNP Report

Basic Info

Name	rs2291739 dbSNP Ensembl
Location	chr12:56420869 - 56420869(1)
Variant Alleles	G/A/C
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.391573
Functional Annotation	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant. Polyphen Annotation: probably damaging(ENST00000229201, ENST00000553532) SIFT Annotation: deleterious(ENST00000229201, ENST00000553532)
Consequence to Transcript	downstream_gene_variant(ENST00000555808); missense_variant(ENST00000229201, ENST00000553532); non_coding_transcript_exon_variant(ENST00000553314, ENST00000557589); non_coding_transcript_variant(ENST00000553314, ENST00000557589)
No. of Studies	2 (Positive: 1; Negative: 1; 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
Mansour, H. A., 2006	A/G		TDT P-value = 0.089, X²=2.89, df=1 in the samples...... TDT P-value = 0.089, X²=2.89, df=1 in the samples combined, Pittsburgh Trends test=0.812 for BDI More...	Another locus in TIMELESS showed substantial but not quite s...... Another locus in TIMELESS showed substantial but not quite significant transmission bias when we analyzed transmission distortion of the bipolar samples jointly. More...	Negative
Dmitrzak-Weglarz, M. P., 2014	T/C		MD (BPD and UPD): P-value=0.0451, FDR=0.3053, OR=1.19, 95%CI...... MD (BPD and UPD): P-value=0.0451, FDR=0.3053, OR=1.19, 95%CI=1.00-1.40. More...	Polymorphisms rs2291739 of TIM gene was associated with MD r...... Polymorphisms rs2291739 of TIM gene was associated with MD risk. More...	Positive

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
ARHGEF5	Rho guanine nucleotide exchange factor (GEF) 5	7q35	1(1/0/0)
TIMELESS	timeless circadian clock	12q13.3	3(0/3/0)

SNPs in LD with rs2291739 (count: 19) View in gBrowse (chr12:56420786..56440089 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs703829	intron_variant	0.925[CEU]; 0.822[TSI]
rs11833581	intron_variant	0.915[CEU]
rs10876889	intron_variant	0.925[CEU]; 0.822[TSI]
rs7312888	intron_variant	0.925[CEU]; 0.869[TSI]
rs11171850	intron_variant	0.929[CEU]
rs12299614	intron_variant	0.925[CEU]; 0.82[TSI]
rs774036	intron_variant	0.923[CEU]
rs774047	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.925[CEU]; 0.822[TSI]
rs774034	intron_variant	0.927[CEU]
rs774039	intron_variant	0.925[CEU]; 0.822[TSI]
rs10876890	intron_variant	0.862[CEU]
rs11171852	intron_variant	0.852[CEU]
rs6581094	intron_variant	0.875[CEU]
rs774033	synonymous_variant	0.925[CEU]; 0.822[TSI]
rs7977477	intron_variant	0.929[CEU]
rs11610921	intron_variant	0.862[CEU]
rs774035	intron_variant	0.927[CEU]
rs812279	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CEU]; 0.886[TSI]
rs774027	missense_variant; upstream_gene_variant	0.929[CEU]

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

Reference	Statistical Result	Description	Result Category
Mansour, H. A., 2006	not analyzed for Pittsburgh SZ/SZA		Negative

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