Variant report

Variant	rs540604011
Chromosome Location	chr3:52089425-52089426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52016320..52018909-chr3:52089400..52091632,2	MCF-7	breast:
2	chr1:149222699..149225112-chr3:52088904..52091700,2	MCF-7	breast:
3	chr3:52087390..52089445-chr3:52228138..52231082,2	K562	blood:
4	chr3:52028061..52031321-chr3:52088873..52092735,5	MCF-7	breast:
5	chr3:52088419..52090155-chr3:52113932..52115849,2	K562	blood:
6	chr3:52026823..52031380-chr3:52087204..52091486,4	K562	blood:
7	chr3:51974895..51976742-chr3:52087202..52089493,2	K562	blood:
8	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:
9	chr3:52088633..52090447-chr3:52187469..52189147,2	MCF-7	breast:
10	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:
11	chr3:52015921..52019600-chr3:52088214..52092499,4	K562	blood:
12	chr3:52088066..52089919-chr3:52114349..52115931,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000162244	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000256097	Chromatin interaction
ENSG00000164087	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1792042	chr3:52070955-52091254	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1793040	chr3:52070955-52091254	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv1797975	chr3:52070955-52091254	Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv1798814	chr3:52070955-52091254	Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
15	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv590281	chr3:52088204-52090396	Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
18	nsv590282	chr3:52088204-52097060	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	esv3355709	chr3:52088937-52091485	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52083200-52090200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:52084800-52090000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:52085000-52090200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:52086200-52090000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr3:52086400-52090200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr3:52086800-52090800	Active TSS	Rectal Smooth Muscle	rectum
7	chr3:52087400-52091800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:52087600-52090800	Enhancers	Fetal Brain Male	brain
9	chr3:52088000-52090200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr3:52088200-52090200	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr3:52088400-52089800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:52088400-52089800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:52088400-52090000	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr3:52088400-52090200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:52088400-52090200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:52088400-52090800	Active TSS	HSMM	muscle
17	chr3:52088600-52089600	Flanking Active TSS	Fetal Thymus	thymus
18	chr3:52088600-52089600	Flanking Active TSS	Thymus	Thymus
19	chr3:52088600-52090000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:52088600-52090200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:52088600-52090200	Flanking Active TSS	Placenta	Placenta
22	chr3:52088600-52090200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr3:52088600-52090800	Active TSS	Brain Anterior Caudate	brain
24	chr3:52088600-52091200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr3:52088600-52091600	Active TSS	Psoas Muscle	Psoas
26	chr3:52088600-52091800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:52088600-52091800	Active TSS	Aorta	Aorta
28	chr3:52088600-52092000	Active TSS	Fetal Kidney	kidney
29	chr3:52088600-52092000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:52088800-52089600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr3:52088800-52089800	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr3:52088800-52089800	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr3:52088800-52089800	Active TSS	Right Atrium	heart
34	chr3:52088800-52090200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:52088800-52090200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr3:52088800-52090200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr3:52088800-52090200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:52088800-52090200	Flanking Active TSS	Colonic Mucosa	Colon
39	chr3:52088800-52090200	Flanking Active TSS	Pancreas	Pancrea
40	chr3:52088800-52090800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52088800-52090800	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr3:52088800-52090800	Active TSS	Esophagus	oesophagus
43	chr3:52088800-52090800	Active TSS	HMEC	breast
44	chr3:52088800-52090800	Active TSS	NHDF-Ad	bronchial
45	chr3:52088800-52091400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:52088800-52091600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52088800-52091600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:52088800-52091600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:52088800-52091600	Active TSS	Brain Substantia Nigra	brain
50	chr3:52088800-52091600	Active TSS	Gastric	stomach

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