Variant report

Variant	rs544184257
Chromosome Location	chr3:48469655-48469656
allele	C/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	chr3:48468563-48472948	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:48468603-48471989	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYBL2	chr3:48469649-48470371	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:48466790-48473062	HepG2	liver:	n/a	n/a
5	HEY1	chr3:48469646-48472042	HepG2	liver:	n/a	chr3:48471229-48471244 chr3:48470221-48470236 chr3:48470955-48470970 chr3:48470572-48470587 chr3:48471347-48471362 chr3:48470953-48470968
6	POLR2A	chr3:48466636-48473218	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:48461949-48470573	HepG2	liver:	n/a	n/a
8	HEY1	chr3:48469356-48473141	HepG2	liver:	n/a	chr3:48471229-48471244 chr3:48470221-48470236 chr3:48470955-48470970 chr3:48470572-48470587 chr3:48471347-48471362 chr3:48470953-48470968
9	POLR2A	chr3:48469582-48472048	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr3:48469655-48469662	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:48469652-48471931	HepG2	liver:	n/a	n/a
12	ZNF263	chr3:48468929-48470023	HEK293-T-REx	kidney:	n/a	n/a
13	REST	chr3:48469446-48471910	H1-neurons	neurons:	n/a	chr3:48471333-48471343 chr3:48471343-48471356 chr3:48469903-48469913 chr3:48470943-48470956 chr3:48469907-48469916 chr3:48471255-48471262 chr3:48470994-48471012
14	CHD2	chr3:48469631-48470083	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:48469643-48471881	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAZ	chr3:48469476-48472061	IMR90	lung:	n/a	chr3:48471053-48471063 chr3:48471085-48471094 chr3:48471081-48471090 chr3:48470436-48470446 chr3:48471214-48471224
17	POLR2A	chr3:48466832-48470960	HepG2	liver:	n/a	n/a
18	NR2F2	chr3:48469324-48473447	HepG2	liver:	n/a	n/a
19	MYBL2	chr3:48469516-48470352	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48468692..48470258-chr3:48540999..48543179,2	K562	blood:
2	chr3:48447403..48451386-chr3:48469064..48473166,5	MCF-7	breast:
3	chr3:48468569..48471339-chr3:48481498..48483135,2	MCF-7	breast:
4	chr3:48469539..48472280-chr3:48487900..48489460,2	MCF-7	breast:
5	chr3:48468825..48473989-chr3:48477233..48479904,8	MCF-7	breast:
6	chr3:48454313..48457718-chr3:48468090..48471775,3	MCF-7	breast:
7	chr3:48449321..48451479-chr3:48469134..48470813,2	K562	blood:
8	chr3:48262147..48265261-chr3:48469207..48471708,3	MCF-7	breast:
9	chr3:48469238..48470766-chr3:48475328..48477578,2	K562	blood:
10	chr3:48342140..48344321-chr3:48467110..48469904,2	K562	blood:
11	chr3:48281213..48283691-chr3:48469389..48472428,3	K562	blood:
12	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
13	chr3:48301212..48303241-chr3:48468487..48470721,2	MCF-7	breast:
14	chr3:48282380..48283987-chr3:48469620..48473031,3	MCF-7	breast:
15	chr3:48469445..48473059-chr3:48486174..48489531,5	MCF-7	breast:

Variant related genes	Relation type
PLXNB1	TF binding region
ENSG00000164048	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000172113	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000164047	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000164054	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	esv3345173	chr3:48469473-48472321	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48466200-48470000	Enhancers	Spleen	Spleen
2	chr3:48466400-48470000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:48466400-48470000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr3:48466600-48469800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr3:48466600-48470000	Enhancers	Placenta	Placenta
6	chr3:48466800-48469800	Flanking Active TSS	Fetal Brain Female	brain
7	chr3:48466800-48469800	Flanking Active TSS	HMEC	breast
8	chr3:48466800-48470000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:48466800-48470200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr3:48467000-48470000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr3:48467000-48470000	Flanking Active TSS	Colon Smooth Muscle	Colon
12	chr3:48467200-48469800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:48467200-48470000	Flanking Active TSS	HSMMtube	muscle
14	chr3:48467200-48470200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:48467400-48470000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:48467600-48469800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:48467800-48471400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:48468000-48470000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:48468000-48470000	Flanking Active TSS	Ovary	ovary
20	chr3:48468000-48470200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:48468000-48471400	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:48468200-48469800	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr3:48468200-48470000	Flanking Active TSS	Liver	Liver
24	chr3:48468200-48470000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:48468200-48470200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:48468200-48470200	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr3:48468400-48469800	Transcr. at gene 5' and 3'	NHEK	skin
28	chr3:48468400-48470200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr3:48468600-48470000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:48468600-48470000	Flanking Active TSS	Colonic Mucosa	Colon
31	chr3:48468600-48470000	Flanking Active TSS	Fetal Intestine Large	intestine
32	chr3:48468600-48470000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr3:48468600-48470200	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr3:48468600-48470200	Flanking Active TSS	HSMM	muscle
35	chr3:48468600-48472000	Active TSS	Fetal Kidney	kidney
36	chr3:48468800-48469800	Enhancers	Right Atrium	heart
37	chr3:48468800-48470000	Flanking Active TSS	Fetal Brain Male	brain
38	chr3:48468800-48470000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
39	chr3:48468800-48470000	Flanking Active TSS	Pancreas	Pancrea
40	chr3:48468800-48470000	Flanking Active TSS	NHDF-Ad	bronchial
41	chr3:48468800-48471800	Active TSS	Aorta	Aorta
42	chr3:48468800-48472000	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr3:48469000-48469800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr3:48469000-48469800	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr3:48469000-48470000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr3:48469000-48470000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:48469000-48470000	Flanking Active TSS	Fetal Heart	heart
48	chr3:48469000-48470000	Flanking Active TSS	Fetal Lung	lung
49	chr3:48469000-48470000	Flanking Active TSS	Hela-S3	cervix
50	chr3:48469000-48470200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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