Variant report

Variant	rs2289346
Chromosome Location	chr3:139169729-139169730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139168645..139171256-chr3:139173067..139176313,3	K562	blood:
2	chr3:139165019..139166769-chr3:139169234..139171368,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10513077	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914638	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11924964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11928018	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12107249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1599926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs182409	1.00[JPT][hapmap]
rs2233817	0.85[CEU][hapmap]
rs2278577	0.87[CEU][hapmap]
rs2289345	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3772874	0.87[CEU][hapmap]
rs56176652	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57459537	0.81[ASN][1000 genomes]
rs58929533	0.88[ASN][1000 genomes]
rs59467986	0.81[ASN][1000 genomes]
rs59583748	0.88[ASN][1000 genomes]
rs60077646	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6439863	0.87[CEU][hapmap]
rs6767503	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6774691	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6781318	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6788896	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797945	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6804069	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808946	0.82[ASN][1000 genomes]
rs72986758	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7373302	0.87[CEU][hapmap]
rs7619827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622961	1.00[JPT][hapmap]
rs7644878	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7649535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7651618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9756378	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9879736	1.00[CEU][hapmap]
rs9879748	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1000519	chr3:139159300-139206245	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2752377	chr3:139163302-139188302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139138600-139170400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:139142200-139172200	Weak transcription	Fetal Heart	heart
3	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
4	chr3:139144800-139173200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:139145200-139170400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:139149800-139170600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:139154200-139171200	Weak transcription	Right Atrium	heart
8	chr3:139154200-139173600	Weak transcription	Ovary	ovary
9	chr3:139154200-139178600	Weak transcription	Left Ventricle	heart
10	chr3:139158600-139172600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:139158600-139174800	Weak transcription	Adipose Nuclei	Adipose
12	chr3:139160200-139174800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:139160600-139170200	Weak transcription	Lung	lung
14	chr3:139160600-139174800	Weak transcription	Fetal Brain Male	brain
15	chr3:139163000-139170000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:139163400-139189000	Weak transcription	Small Intestine	intestine
17	chr3:139163800-139180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:139165800-139178600	Weak transcription	Right Ventricle	heart
19	chr3:139166000-139179000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:139167000-139175400	Weak transcription	Fetal Brain Female	brain
21	chr3:139167400-139170400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:139167400-139170600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:139167400-139173200	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:139167400-139174800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:139167400-139176000	Weak transcription	Brain Anterior Caudate	brain
26	chr3:139167600-139170200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:139167600-139173400	Weak transcription	Brain Germinal Matrix	brain
28	chr3:139168000-139175200	Weak transcription	Brain Angular Gyrus	brain
29	chr3:139168200-139170200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:139168200-139170200	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:139168400-139170200	Weak transcription	Brain Substantia Nigra	brain
32	chr3:139168600-139170000	Enhancers	HepG2	liver
33	chr3:139168600-139196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:139168800-139170200	Enhancers	Fetal Intestine Large	intestine
35	chr3:139169200-139172200	Enhancers	HSMMtube	muscle
36	chr3:139169200-139175000	Genic enhancers	Fetal Intestine Small	intestine
37	chr3:139169400-139173400	Weak transcription	Pancreas	Pancrea

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