Variant report

Variant	rs28718940
Chromosome Location	chr3:120140763-120140764
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	chr3:120140370..120142794-chr3:120168186..120170876,2	MCF-7	breast:
2	chr3:120139169..120141302-chr3:120275834..120278046,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163430	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1147697	1.00[ASN][1000 genomes]
rs1700	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28487977	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6799005	0.85[AMR][1000 genomes]
rs9810151	1.00[ASN][1000 genomes]
rs9860676	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
2	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:120135400-120151600	Genic enhancers	Osteobl	bone
4	chr3:120135600-120141600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:120136800-120140800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr3:120136800-120140800	Enhancers	Brain Substantia Nigra	brain
7	chr3:120136800-120140800	Genic enhancers	HSMM	muscle
8	chr3:120136800-120141000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:120136800-120141200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:120136800-120141200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:120136800-120141200	Enhancers	Brain Angular Gyrus	brain
12	chr3:120136800-120141200	Enhancers	Brain Hippocampus Middle	brain
13	chr3:120136800-120141200	Enhancers	Fetal Lung	lung
14	chr3:120136800-120141600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:120136800-120141800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:120136800-120141800	Enhancers	Fetal Heart	heart
17	chr3:120136800-120142200	Enhancers	Colon Smooth Muscle	Colon
18	chr3:120136800-120142600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:120136800-120145200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:120136800-120147400	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr3:120136800-120147600	Enhancers	Adipose Nuclei	Adipose
22	chr3:120136800-120148400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:120136800-120148600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:120137000-120140800	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:120137000-120141200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:120137000-120149600	Enhancers	Rectal Smooth Muscle	rectum
27	chr3:120137400-120141400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:120137600-120142000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:120137800-120142600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:120138200-120141200	Genic enhancers	NH-A	brain
33	chr3:120138200-120142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:120138200-120142000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:120138200-120142000	Weak transcription	Lung	lung
36	chr3:120138200-120142200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:120138200-120145400	Weak transcription	NHEK	skin
38	chr3:120138200-120146400	Weak transcription	Fetal Intestine Large	intestine
39	chr3:120138200-120154200	Weak transcription	HMEC	breast
40	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:120138200-120169200	Weak transcription	Gastric	stomach
44	chr3:120138400-120143000	Weak transcription	Fetal Thymus	thymus
45	chr3:120138400-120148600	Genic enhancers	NHDF-Ad	bronchial
46	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
47	chr3:120138600-120141200	Enhancers	NHLF	lung
48	chr3:120138600-120147800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:120138600-120148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:120138800-120141000	Genic enhancers	Muscle Satellite Cultured Cells	--

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