Variant report

Variant	rs2871747
Chromosome Location	chr3:79062087-79062088
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:79061171..79063415-chr3:79068475..79070021,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169855	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11127638	1.00[EUR][1000 genomes]
rs11923198	1.00[EUR][1000 genomes]
rs12495750	1.00[EUR][1000 genomes]
rs13096526	0.86[EUR][1000 genomes]
rs1349023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1349024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1374883	1.00[EUR][1000 genomes]
rs1374885	0.86[EUR][1000 genomes]
rs1374886	0.86[EUR][1000 genomes]
rs1374887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1374888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1374889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1900663	0.86[EUR][1000 genomes]
rs1947154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4680946	0.86[EUR][1000 genomes]
rs61586777	0.86[EUR][1000 genomes]
rs6548603	1.00[EUR][1000 genomes]
rs6548604	0.86[EUR][1000 genomes]
rs6548605	0.86[EUR][1000 genomes]
rs6548606	0.86[EUR][1000 genomes]
rs6774082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6788693	1.00[EUR][1000 genomes]
rs6797152	1.00[EUR][1000 genomes]
rs6804234	0.86[EUR][1000 genomes]
rs7625043	0.86[EUR][1000 genomes]
rs7646169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845900	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834745	chr3:79055426-79227937	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:79044800-79064600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:79054400-79066600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:79054600-79064600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:79058600-79064600	Enhancers	Brain Hippocampus Middle	brain
5	chr3:79059000-79064800	Enhancers	Brain Substantia Nigra	brain
6	chr3:79060000-79062400	Enhancers	HepG2	liver
7	chr3:79060000-79064600	Enhancers	Fetal Lung	lung
8	chr3:79060400-79062400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:79060600-79062400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:79060600-79064600	Weak transcription	Fetal Stomach	stomach
11	chr3:79060800-79064400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:79061000-79062200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr3:79061000-79063600	Enhancers	Colon Smooth Muscle	Colon
14	chr3:79061000-79064600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:79061200-79062200	Enhancers	Adipose Nuclei	Adipose
16	chr3:79061200-79062600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:79061200-79063000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:79061200-79064200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:79061200-79067000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:79061400-79062200	Enhancers	Brain Anterior Caudate	brain
21	chr3:79061400-79062600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:79061400-79062600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:79061400-79062800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:79061400-79064200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:79061400-79065800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:79061600-79062200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:79061600-79062600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:79061600-79062600	Enhancers	Fetal Kidney	kidney
29	chr3:79061600-79064000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:79061800-79062200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr3:79061800-79062200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:79061800-79062200	Flanking Active TSS	Fetal Brain Male	brain
33	chr3:79061800-79062200	Enhancers	Fetal Heart	heart
34	chr3:79061800-79062200	Active TSS	GM12878-XiMat	blood
35	chr3:79061800-79062400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:79061800-79062400	Enhancers	Primary T cells from cord blood	blood
37	chr3:79061800-79062400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:79061800-79062400	Enhancers	Psoas Muscle	Psoas
39	chr3:79061800-79062400	Enhancers	Right Atrium	heart
40	chr3:79061800-79062600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:79061800-79062600	Enhancers	H9 Cell Line	embryonic stem cell
42	chr3:79061800-79062600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:79061800-79062600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:79061800-79062600	Enhancers	Aorta	Aorta
45	chr3:79061800-79062600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:79061800-79062600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr3:79061800-79062600	Flanking Active TSS	Fetal Brain Female	brain
48	chr3:79061800-79062600	Enhancers	Rectal Smooth Muscle	rectum
49	chr3:79061800-79063600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:79062000-79062200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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