Variant report

Variant	rs11720866
Chromosome Location	chr3:52277738-52277739
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52277359-52278451	K562	blood:	n/a	n/a
2	MTA3	chr3:52277652-52279590	GM12878	blood:	n/a	n/a
3	SETDB1	chr3:52277232-52278048	U2OS	brain:	n/a	n/a
4	WRNIP1	chr3:52277639-52277843	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:52277713-52280381	GM18505	blood:	n/a	n/a
6	KAP1	chr3:52277483-52277901	HEK293	kidney:	n/a	n/a
7	MTA3	chr3:52277397-52279759	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:52277466-52280409	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:52277692-52280195	GM12878	blood:	n/a	n/a
10	NFATC1	chr3:52277464-52278793	GM12878	blood:	n/a	n/a
11	RELA	chr3:52277557-52279708	GM18951	blood:	n/a	n/a
12	POLR2A	chr3:52277475-52278652	HCT-116	colon:	n/a	n/a
13	POLR2A	chr3:52277594-52278578	Raji	blood:	n/a	n/a
14	RELA	chr3:52277720-52278717	GM18505	blood:	n/a	n/a
15	SPI1	chr3:52277709-52278773	HL-60	blood:	n/a	chr3:52278471-52278484
16	NFATC1	chr3:52277579-52278796	GM12878	blood:	n/a	n/a
17	MAX	chr3:52277685-52277798	NB4	blood:	n/a	chr3:52277734-52277745 chr3:52277735-52277745
18	CBX3	chr3:52277461-52277851	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52277680..52279387-chr3:52372909..52375320,2	K562	blood:
2	chr3:52277093..52279461-chr3:52290667..52292256,2	MCF-7	breast:

Variant related genes	Relation type
PPM1M	TF binding region
TWF2	TF binding region
TLR9	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11707938	0.91[EUR][1000 genomes]
rs56296139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73082798	1.00[AFR][1000 genomes]
rs73088787	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52274400-52278800	Weak transcription	Fetal Lung	lung
2	chr3:52274400-52279000	Weak transcription	Fetal Heart	heart
3	chr3:52274400-52279400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52274600-52278000	Weak transcription	Esophagus	oesophagus
5	chr3:52274600-52278200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:52274600-52278400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:52274600-52279000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:52274600-52279000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:52274800-52277800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:52274800-52278000	Weak transcription	Left Ventricle	heart
11	chr3:52274800-52278200	Weak transcription	Colonic Mucosa	Colon
12	chr3:52274800-52278600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:52274800-52278800	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:52274800-52279200	Weak transcription	Liver	Liver
15	chr3:52274800-52279200	Weak transcription	Pancreas	Pancrea
16	chr3:52274800-52279200	Weak transcription	Right Atrium	heart
17	chr3:52275000-52277800	Weak transcription	NH-A	brain
18	chr3:52275000-52278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:52275000-52278000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:52275000-52278000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:52275000-52278000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:52275000-52278000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:52275000-52278000	Weak transcription	Right Ventricle	heart
24	chr3:52275000-52278000	Weak transcription	HSMMtube	muscle
25	chr3:52275000-52278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:52275000-52279000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:52275000-52279200	Weak transcription	Stomach Mucosa	stomach
28	chr3:52275200-52277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:52275200-52277800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:52275200-52277800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:52275200-52277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:52275200-52277800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:52275200-52277800	Weak transcription	NHEK	skin
34	chr3:52275200-52278000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:52275200-52278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:52275200-52278000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:52275200-52278000	Weak transcription	NHDF-Ad	bronchial
38	chr3:52275200-52278000	Weak transcription	Osteobl	bone
39	chr3:52275200-52278200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:52275200-52278200	Weak transcription	Adipose Nuclei	Adipose
41	chr3:52275200-52278200	Weak transcription	Dnd41	blood
42	chr3:52275200-52278200	Weak transcription	HepG2	liver
43	chr3:52275200-52278400	Weak transcription	NHLF	lung
44	chr3:52275200-52279000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:52275200-52279000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:52275200-52279000	Weak transcription	Brain Substantia Nigra	brain
47	chr3:52275200-52279000	Weak transcription	A549	lung
48	chr3:52275200-52279200	Weak transcription	HSMM	muscle
49	chr3:52275200-52279400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:52275400-52277800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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