Variant report

Variant	rs4564921
Chromosome Location	chr3:139278558-139278559
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139270060..139271651-chr3:139277241..139279414,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10935331	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs176990	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs190910	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs211586	0.82[EUR][1000 genomes]
rs295501	0.90[EUR][1000 genomes]
rs6797111	0.85[EUR][1000 genomes]
rs9816597	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9825927	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9826668	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139259200-139307000	Weak transcription	Aorta	Aorta
2	chr3:139261200-139279400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:139265800-139290600	Weak transcription	Adipose Nuclei	Adipose
4	chr3:139268400-139292200	Weak transcription	Right Atrium	heart
5	chr3:139271600-139279200	Weak transcription	Left Ventricle	heart
6	chr3:139271800-139279400	Weak transcription	Fetal Intestine Large	intestine
7	chr3:139271800-139279400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:139271800-139293000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:139272600-139279000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:139273200-139290600	Weak transcription	Gastric	stomach
11	chr3:139273600-139292600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:139273800-139282600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:139274400-139290800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:139274800-139281200	Weak transcription	Fetal Lung	lung
15	chr3:139274800-139282400	Weak transcription	Fetal Stomach	stomach
16	chr3:139275000-139279400	Weak transcription	Ovary	ovary
17	chr3:139275000-139280600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:139275000-139290600	Weak transcription	Lung	lung
19	chr3:139275400-139279400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:139275800-139279800	Weak transcription	Spleen	Spleen
21	chr3:139276000-139292400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:139276000-139299400	Weak transcription	Primary T cells from cord blood	blood
23	chr3:139276600-139280400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:139276800-139279400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:139276800-139290600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:139277000-139279200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:139277200-139278800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:139277200-139280000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:139277200-139280800	Enhancers	HMEC	breast
30	chr3:139277400-139279400	Enhancers	NHEK	skin
31	chr3:139277400-139280200	Enhancers	NH-A	brain
32	chr3:139277600-139278600	Enhancers	Pancreas	Pancrea
33	chr3:139277600-139278800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:139277600-139278800	Enhancers	Brain Germinal Matrix	brain
35	chr3:139277600-139279000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:139277600-139279600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:139277800-139281000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:139277800-139290600	Weak transcription	Liver	Liver
39	chr3:139278000-139279200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:139278000-139280200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:139278000-139292200	Weak transcription	Right Ventricle	heart
42	chr3:139278200-139278600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:139278200-139278800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:139278200-139279000	Enhancers	Fetal Kidney	kidney
45	chr3:139278400-139278600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr3:139278400-139278800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr3:139278400-139278800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:139278400-139281000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:139278400-139290600	Weak transcription	Esophagus	oesophagus

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