Variant report

Variant	rs557999939
Chromosome Location	chr5:179232192-179232193
allele	-/A
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179231901-179232274	ProgFib	skin:	n/a	n/a
2	POLR2A	chr5:179232175-179232907	K562	blood:	n/a	n/a
3	POLR2A	chr5:179232087-179232320	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:179231795-179232467	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:179224667-179233676	HL-60	blood:	n/a	n/a
6	MAX	chr5:179232077-179232267	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:179230590-179233696	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:179232156-179232597	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr5:179232184-179232219	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:179230770-179234550	Hela-S3	cervix:	n/a	n/a
11	EBF1	chr5:179232048-179232362	GM12878	blood:	n/a	n/a
12	MXI1	chr5:179232019-179234611	IMR90	lung:	n/a	n/a
13	TCF12	chr5:179231946-179232633	A549	lung:	n/a	n/a
14	POLR2A	chr5:179231916-179232582	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:179232117-179232278	MCF-7	breast:	n/a	n/a
16	POLR2A	chr5:179231839-179234641	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:179232134-179234679	PFSK-1	brain:	n/a	n/a
18	MXI1	chr5:179232105-179232877	Hela-S3	cervix:	n/a	n/a
19	TBP	chr5:179232144-179232471	Hela-S3	cervix:	n/a	n/a
20	CHD2	chr5:179232055-179233585	Hela-S3	cervix:	n/a	chr5:179233354-179233364
21	POLR2A	chr5:179231997-179232257	GM12891	blood:	n/a	n/a
22	MXI1	chr5:179231675-179234766	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr5:179228779-179234761	K562	blood:	n/a	n/a
24	MAX	chr5:179231886-179234746	A549	lung:	n/a	chr5:179232753-179232763 chr5:179232882-179232892 chr5:179233343-179233353
25	POLR2A	chr5:179232065-179234550	Raji	blood:	n/a	n/a
26	SMARCB1	chr5:179232127-179234584	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:179231922-179234638	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr5:179232034-179233686	Hela-S3	cervix:	n/a	n/a
29	ZNF263	chr5:179231727-179232864	HEK293-T-REx	kidney:	n/a	chr5:179231999-179232020
30	CREB1	chr5:179231978-179234626	HepG2	liver:	n/a	n/a
31	POLR2A	chr5:179231633-179232708	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:179229521-179234618	MCF-7	breast:	n/a	n/a
33	POLR2A	chr5:179231931-179232785	PBDE	blood:	n/a	n/a
34	MAX	chr5:179231894-179233669	HepG2	liver:	n/a	chr5:179232753-179232763 chr5:179232882-179232892 chr5:179233343-179233353
35	MXI1	chr5:179232102-179233573	HepG2	liver:	n/a	n/a
36	BCL3	chr5:179232078-179232689	A549	lung:	n/a	n/a
37	POLR2A	chr5:179231806-179232446	HepG2	liver:	n/a	n/a
38	YY1	chr5:179232139-179232617	HepG2	liver:	n/a	chr5:179232532-179232543
39	POLR2A	chr5:179224688-179234670	K562	blood:	n/a	n/a
40	POLR2A	chr5:179231534-179232263	HepG2	liver:	n/a	n/a
41	POLR2A	chr5:179232028-179234595	MCF-7	breast:	n/a	n/a
42	ELF1	chr5:179231990-179233068	MCF-7	breast:	n/a	chr5:179232952-179232964 chr5:179232879-179232891
43	POLR2A	chr5:179231819-179235745	HepG2	liver:	n/a	n/a
44	MAX	chr5:179232077-179234085	Hela-S3	cervix:	n/a	chr5:179232753-179232763 chr5:179232882-179232892 chr5:179233343-179233353
45	POLR2A	chr5:179231910-179232363	HepG2	liver:	n/a	n/a
46	MAX	chr5:179232006-179233695	MCF-7	breast:	n/a	chr5:179232753-179232763 chr5:179232882-179232892 chr5:179233343-179233353

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:179232165-179232215	GM12878	blood:	n/a
2	chr5:179232165-179232215	HCM	heart:	n/a
3	chr5:179232165-179232215	AoSMC	blood vessel:	n/a
4	chr5:179232165-179232215	Jurkat	blood:	n/a
5	chr5:179232165-179232215	AG10803	skin:	n/a
6	chr5:179232165-179232215	HPAEpiC	pulmonary alveolar:	n/a
7	chr5:179232165-179232215	PFSK-1	brain:	n/a
8	chr5:179232165-179232215	NB4	blood:	n/a
9	chr5:179232165-179232215	BJ	skin:	n/a
10	chr5:179232165-179232215	Caco-2	colon:	n/a
11	chr5:179232165-179232215	ProgFib	skin:	n/a
12	chr5:179232165-179232215	IMR90	lung:	fetal
13	chr5:179232165-179232215	U87	brain:	n/a
14	chr5:179232165-179232215	HMEC	breast:	n/a
15	chr5:179232165-179232215	CMK	blood:	n/a
16	chr5:179232165-179232215	HCPEpiC	choroid plexus:	n/a
17	chr5:179232165-179232215	SKMC	muscle:	n/a
18	chr5:179232165-179232215	MCF-7	breast:	n/a
19	chr5:179232165-179232215	ECC-1	luminal epithelium:	n/a
20	chr5:179232165-179232215	AG04449	skin:	fetal
21	chr5:179232165-179232215	ovcar-3	ovarian:	n/a
22	chr5:179232165-179232215	H1-hESC	embryonic stem cell:	embryo
23	chr5:179232165-179232215	HRPEpiC	eye:	n/a
24	chr5:179232165-179232215	PrEC	prostate:	n/a
25	chr5:179232165-179232215	AG09309	skin:	n/a
26	chr5:179232165-179232215	BE2_C	brain:	n/a
27	chr5:179232165-179232215	SK-N-MC	brain:	n/a
28	chr5:179232165-179232215	HRCEpiC	kidney:	n/a
29	chr5:179232165-179232215	NH-A	brain:	n/a
30	chr5:179232165-179232215	GM12892	blood:	n/a
31	chr5:179232165-179232215	HRE	kidney:	n/a
32	chr5:179232165-179232215	Hela-S3	cervix:	n/a
33	chr5:179232165-179232215	HCF	heart:	n/a
34	chr5:179232165-179232215	HUVEC	blood vessel:	n/a
35	chr5:179232165-179232215	T-47D	breast:	n/a
36	chr5:179232165-179232215	MCF10A-Er-Src	breast:	n/a
37	chr5:179232165-179232215	GM06990	blood:	n/a
38	chr5:179232165-179232215	SK-N-SH_RA	brain:	n/a
39	chr5:179232165-179232215	AG09319	gingival:	n/a
40	chr5:179232165-179232215	NT2-D1	testis:	n/a
41	chr5:179232165-179232215	SK-N-SH	brain:	n/a
42	chr5:179232165-179232215	K562	blood:	n/a
43	chr5:179232165-179232215	HNPCEpiC	eye:	n/a
44	chr5:179232165-179232215	GM19239	blood:	n/a
45	chr5:179232165-179232215	AG04450	lung:	fetal
46	chr5:179232165-179232215	HIPEpiC	eye:	n/a
47	chr5:179232165-179232215	PANC-1	pancreas:	n/a
48	chr5:179232165-179232215	HEK293	kidney:	embryo
49	chr5:179232165-179232215	SAEC	small airway:	n/a
50	chr5:179232165-179232215	GM12891	blood:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179231951..179234998-chr5:179332268..179335922,5	MCF-7	breast:
2	chr5:179229039..179235504-chr5:179284286..179287391,9	MCF-7	breast:
3	chr5:179231022..179234564-chr5:179332456..179334964,4	MCF-7	breast:
4	chr5:179049195..179052432-chr5:179232038..179235083,3	K562	blood:
5	chr5:179103716..179105834-chr5:179232132..179234075,2	MCF-7	breast:
6	chr5:179123960..179129281-chr5:179231995..179235216,8	K562	blood:
7	chr5:179048743..179051829-chr5:179229515..179233744,4	MCF-7	breast:
8	chr5:179158130..179161320-chr5:179231546..179235366,4	K562	blood:
9	chr5:179123960..179129252-chr5:179231413..179236095,7	K562	blood:
10	chr5:179194648..179196545-chr5:179230223..179233407,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf45-4	chr5:179231941-179232385	NONHSAT105628

No data

Variant related genes	Relation type
SQSTM1	TF binding region
MGAT4B	TF binding region
SQSTM1	CpG island
MGAT4B	CpG island
ENSG00000161010	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv883285	chr5:179223023-179238794	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	153 gene(s)	inside rSNPs	diseases
17	nsv600668	chr5:179227865-179242581	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	esv3403342	chr5:179231746-179236044	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179224000-179232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:179226200-179232200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:179226800-179233200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179227800-179232200	Enhancers	Fetal Heart	heart
5	chr5:179228000-179232400	Weak transcription	Aorta	Aorta
6	chr5:179228400-179232400	Genic enhancers	Placenta	Placenta
7	chr5:179228600-179232200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:179228800-179232200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:179228800-179232200	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr5:179228800-179232400	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:179228800-179232400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:179228800-179232400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:179228800-179232400	Enhancers	Fetal Thymus	thymus
14	chr5:179229400-179232200	Enhancers	Left Ventricle	heart
15	chr5:179229400-179232400	Enhancers	Primary B cells from cord blood	blood
16	chr5:179229600-179232200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:179230000-179232200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:179230000-179232200	Enhancers	Primary T cells from cord blood	blood
19	chr5:179230000-179232400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:179230000-179232800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:179230200-179232400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:179230200-179232400	Enhancers	Fetal Lung	lung
23	chr5:179230200-179232400	Enhancers	Thymus	Thymus
24	chr5:179230400-179232400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:179230400-179232600	Flanking Active TSS	HepG2	liver
26	chr5:179230400-179232800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr5:179230600-179232200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:179230600-179232200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:179230600-179232200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:179230600-179232400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr5:179230600-179232400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:179230600-179232800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr5:179230800-179232400	Enhancers	Right Atrium	heart
34	chr5:179230800-179232400	Enhancers	Small Intestine	intestine
35	chr5:179230800-179232600	Genic enhancers	Spleen	Spleen
36	chr5:179230800-179232600	Flanking Active TSS	GM12878-XiMat	blood
37	chr5:179230800-179232800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr5:179230800-179232800	Enhancers	Fetal Brain Male	brain
39	chr5:179230800-179233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:179231000-179232200	Enhancers	Brain Cingulate Gyrus	brain
41	chr5:179231000-179232600	Flanking Active TSS	Liver	Liver
42	chr5:179231000-179232800	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr5:179231200-179232200	Enhancers	Brain Anterior Caudate	brain
44	chr5:179231200-179232400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:179231200-179232400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
46	chr5:179231200-179232800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr5:179231200-179233200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr5:179231400-179232200	Enhancers	H1 Cell Line	embryonic stem cell
49	chr5:179231400-179232200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:179231400-179232200	Genic enhancers	Right Ventricle	heart

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