Variant report

Variant	rs116280439
Chromosome Location	chr5:179222128-179222129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179221024-179224534	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:179222062-179224315	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:179221940-179224212	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr5:179221992-179223990	HepG2	liver:	n/a	chr5:179223974-179223983
5	POLR2A	chr5:179221174-179222543	PANC-1	pancreas:	n/a	n/a
6	CTCF	chr5:179222060-179222210	Caco-2	colon:	n/a	n/a
7	RUNX3	chr5:179222110-179222496	GM12878	blood:	n/a	n/a
8	SIN3A	chr5:179222118-179222577	H1-hESC	embryonic stem cell:	n/a	n/a
9	HDAC2	chr5:179222112-179224003	MCF-7	breast:	n/a	n/a
10	POLR2A	chr5:179221485-179224536	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:179222006-179224641	HL-60	blood:	n/a	n/a
12	POLR2A	chr5:179220422-179223040	GM12892	blood:	n/a	n/a
13	POLR2A	chr5:179221497-179224609	K562	blood:	n/a	n/a
14	POLR2A	chr5:179221453-179224419	GM12892	blood:	n/a	n/a
15	POLR2A	chr5:179222067-179222462	GM12892	blood:	n/a	n/a
16	NR2F2	chr5:179222044-179224529	MCF-7	breast:	n/a	n/a
17	MTA3	chr5:179222034-179222415	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:179222066-179222207	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:179221554-179222604	K562	blood:	n/a	n/a
20	ZNF263	chr5:179221932-179223912	HEK293-T-REx	kidney:	n/a	chr5:179222558-179222579
21	POLR2A	chr5:179221742-179222288	GM12892	blood:	n/a	n/a
22	CTCF	chr5:179222060-179222210	HEK293	kidney:	n/a	n/a
23	MAX	chr5:179222079-179224128	MCF-7	breast:	n/a	chr5:179223974-179223983
24	ZEB1	chr5:179221804-179224001	HepG2	liver:	n/a	chr5:179223875-179223882
25	POLR2A	chr5:179222070-179222400	K562	blood:	n/a	n/a
26	POLR2A	chr5:179222037-179222503	HepG2	liver:	n/a	n/a
27	MXI1	chr5:179222006-179224002	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr5:179222060-179222210	GM12872	blood:	n/a	n/a
29	POLR2A	chr5:179220850-179224671	K562	blood:	n/a	n/a
30	JUND	chr5:179222027-179224121	MCF-7	breast:	n/a	chr5:179223987-179223995 chr5:179223986-179223996 chr5:179223986-179223996
31	POLR2A	chr5:179221919-179223052	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:179221596-179222519	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr5:179221997-179222338	H1-neurons	neurons:	n/a	n/a
34	ELF1	chr5:179221722-179224051	GM12878	blood:	n/a	n/a
35	CREB1	chr5:179222109-179223993	HepG2	liver:	n/a	n/a
36	POLR2A	chr5:179222054-179223856	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr5:179221560-179224673	GM12878	blood:	n/a	n/a
38	GABPA	chr5:179222116-179223914	MCF-7	breast:	n/a	n/a
39	CTCF	chr5:179222020-179222170	GM12875	blood:	n/a	n/a
40	POLR2A	chr5:179221974-179222326	GM12891	blood:	n/a	n/a
41	MAZ	chr5:179221957-179224240	IMR90	lung:	n/a	chr5:179223974-179223983
42	POLR2A	chr5:179221403-179223894	GM12891	blood:	n/a	n/a
43	POLR2A	chr5:179221985-179224611	MCF-7	breast:	n/a	n/a
44	POLR2A	chr5:179221493-179224465	GM12891	blood:	n/a	n/a
45	POLR2A	chr5:179222012-179222325	H1-hESC	embryonic stem cell:	n/a	n/a
46	SIN3AK20	chr5:179221992-179224001	MCF-7	breast:	n/a	n/a
47	CTCF	chr5:179222020-179222170	HepG2	liver:	n/a	n/a
48	POLR2A	chr5:179222060-179223931	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr5:179221699-179222144	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr5:179219447-179224493	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:179048548..179052839-chr5:179221765..179224480,6	MCF-7	breast:
2	chr5:179123572..179126776-chr5:179221240..179224069,3	MCF-7	breast:
3	chr5:179157523..179162988-chr5:179219694..179224698,13	MCF-7	breast:
4	chr5:179104088..179107429-chr5:179222108..179224529,3	MCF-7	breast:
5	chr5:179158179..179161014-chr5:179220671..179223680,5	MCF-7	breast:
6	chr5:179126009..179127718-chr5:179220885..179222493,2	K562	blood:
7	chr5:179123773..179127716-chr5:179220848..179225521,8	MCF-7	breast:
8	chr5:179104067..179106595-chr5:179220718..179223236,3	MCF-7	breast:
9	chr5:179049356..179051389-chr5:179221894..179224407,2	MCF-7	breast:
10	chr5:179124990..179127718-chr5:179220717..179222385,2	K562	blood:
11	chr5:179221892..179226661-chr5:179285311..179287197,6	MCF-7	breast:
12	chr5:179221198..179223904-chr5:179283563..179286738,3	MCF-7	breast:

No data

Variant related genes	Relation type
LTC4S	TF binding region
ENSG00000169045	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000245317	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats 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	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
10	nsv823361	chr5:179213324-179251243	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
11	nsv600659	chr5:179214251-179225594	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	147 gene(s)	inside rSNPs	diseases
12	nsv600660	chr5:179214251-179231248	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
13	nsv883278	chr5:179214818-179238794	Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
14	nsv883279	chr5:179214818-179248774	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
15	nsv870188	chr5:179218824-179235424	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
16	nsv600661	chr5:179220010-179228623	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
17	nsv600662	chr5:179220010-179231248	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
18	nsv883280	chr5:179220010-179238794	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
19	nsv883281	chr5:179220010-179250500	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
20	nsv883282	chr5:179220638-179231248	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
21	nsv883283	chr5:179220638-179231681	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
22	nsv883284	chr5:179220638-179246415	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	158 gene(s)	inside rSNPs	diseases
23	esv3405621	chr5:179221771-179224319	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
24	nsv600663	chr5:179221789-179228369	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	148 gene(s)	inside rSNPs	diseases
25	nsv600664	chr5:179221789-179228623	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	149 gene(s)	inside rSNPs	diseases
26	nsv600665	chr5:179221789-179231248	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
27	nsv600666	chr5:179221789-179231681	Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179207600-179222200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:179207600-179222600	Weak transcription	Aorta	Aorta
3	chr5:179207800-179222200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:179209400-179222200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:179215600-179223200	Weak transcription	HSMMtube	muscle
6	chr5:179218600-179222800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:179219400-179222200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:179219400-179222400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr5:179219400-179222400	Enhancers	Primary B cells from cord blood	blood
10	chr5:179219600-179222400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:179219600-179222400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:179219600-179222800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:179219800-179222200	Weak transcription	Fetal Brain Female	brain
14	chr5:179220000-179222200	Enhancers	Fetal Lung	lung
15	chr5:179220000-179223000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:179220200-179222200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr5:179220200-179222200	Weak transcription	Brain Germinal Matrix	brain
18	chr5:179220200-179222200	Enhancers	Pancreas	Pancrea
19	chr5:179220200-179222200	Enhancers	Stomach Mucosa	stomach
20	chr5:179220200-179222400	Enhancers	Primary T cells from cord blood	blood
21	chr5:179220200-179222400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr5:179220200-179223800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr5:179220400-179222200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr5:179220400-179222200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr5:179220400-179222600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:179220400-179222600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr5:179220600-179222200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr5:179220600-179222400	Enhancers	Primary B cells from peripheral blood	blood
29	chr5:179220600-179222400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:179220600-179222400	Enhancers	NHLF	lung
31	chr5:179220600-179223000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr5:179220600-179223000	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr5:179220600-179224200	Weak transcription	K562	blood
34	chr5:179220800-179222200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr5:179220800-179222200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:179221000-179222200	Enhancers	Colon Smooth Muscle	Colon
37	chr5:179221000-179222200	Genic enhancers	Fetal Intestine Small	intestine
38	chr5:179221000-179222400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr5:179221000-179223000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr5:179221000-179223000	Flanking Active TSS	Colonic Mucosa	Colon
41	chr5:179221000-179223000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr5:179221000-179223600	Active TSS	Brain Substantia Nigra	brain
43	chr5:179221200-179222200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:179221200-179222200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:179221200-179222200	Enhancers	Primary hematopoietic stem cells	blood
46	chr5:179221200-179222200	Enhancers	Brain Anterior Caudate	brain
47	chr5:179221200-179222200	Enhancers	Fetal Intestine Large	intestine
48	chr5:179221200-179222400	Bivalent Enhancer	Fetal Thymus	thymus
49	chr5:179221200-179222400	Enhancers	Ovary	ovary
50	chr5:179221200-179222400	Weak transcription	NH-A	brain

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