Variant report

Variant	rs542549433
Chromosome Location	chr3:52280779-52280780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:52279829-52280831	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52279887-52284777	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:52280682-52281148	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:52280710-52280816	K562	blood:	n/a	n/a
5	SPI1	chr3:52280722-52281179	HL-60	blood:	n/a	n/a
6	POLR2A	chr3:52280752-52284781	A549	lung:	n/a	n/a
7	POLR2A	chr3:52280659-52281598	GM12892	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52278055..52281861-chr3:52310588..52314481,6	K562	blood:
2	chr3:52278277..52281486-chr3:52282865..52288389,9	K562	blood:
3	chr3:52278055..52281861-chr3:52310505..52315451,9	K562	blood:
4	chr3:52280316..52283002-chr3:52418190..52421140,2	K562	blood:
5	chr3:52278407..52281355-chr3:52281666..52283628,3	MCF-7	breast:
6	chr3:52279829..52282973-chr3:52309699..52312689,5	MCF-7	breast:
7	chr3:52278070..52281652-chr3:52320199..52323338,4	MCF-7	breast:
8	chr3:52278312..52281288-chr3:52312020..52314246,3	MCF-7	breast:

No data

Variant related genes	Relation type
PPM1M	TF binding region
ENSG00000114841	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000164088	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	esv3369308	chr3:52279062-52280960	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52277600-52282000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr3:52278800-52280800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:52278800-52281400	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:52279000-52281400	Flanking Active TSS	Dnd41	blood
5	chr3:52279000-52281400	Active TSS	Osteobl	bone
6	chr3:52279000-52281800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:52279200-52280800	Active TSS	Right Atrium	heart
8	chr3:52279400-52281000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:52279600-52281000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:52279600-52281200	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr3:52279600-52281200	Active TSS	Stomach Mucosa	stomach
12	chr3:52279600-52281600	Active TSS	Brain Substantia Nigra	brain
13	chr3:52279600-52287400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:52280000-52280800	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr3:52280000-52280800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:52280000-52280800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:52280000-52280800	Flanking Active TSS	Liver	Liver
18	chr3:52280000-52280800	Flanking Active TSS	Fetal Muscle Trunk	muscle
19	chr3:52280000-52280800	Flanking Active TSS	NHLF	lung
20	chr3:52280000-52281000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:52280000-52281000	Flanking Active TSS	Placenta	Placenta
22	chr3:52280000-52281200	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr3:52280000-52281200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr3:52280000-52281200	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr3:52280000-52281200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr3:52280000-52281400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr3:52280000-52281400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:52280000-52281400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:52280000-52281400	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr3:52280000-52281400	Flanking Active TSS	Fetal Thymus	thymus
31	chr3:52280000-52281400	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr3:52280000-52281600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr3:52280000-52281600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr3:52280000-52281800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr3:52280000-52281800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr3:52280000-52281800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:52280000-52281800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr3:52280200-52280800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:52280200-52280800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:52280200-52280800	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr3:52280200-52280800	Flanking Active TSS	NHEK	skin
42	chr3:52280200-52281000	Flanking Active TSS	Hela-S3	cervix
43	chr3:52280200-52281200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:52280200-52281200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:52280200-52281200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:52280200-52281400	Enhancers	Placenta Amnion	Placenta Amnion
47	chr3:52280200-52281600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:52280200-52281600	Flanking Active TSS	GM12878-XiMat	blood
49	chr3:52280200-52281800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:52280200-52281800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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