Variant report

Variant	rs4513706
Chromosome Location	chr5:42909290-42909291
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:147)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:147 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:42909031-42909314	LNCaP	prostate:	n/a	n/a
2	ZNF143	chr5:42908971-42909361	K562	blood:	n/a	n/a
3	MYC	chr5:42908648-42909398	K562	blood:	n/a	n/a
4	RAD21	chr5:42908868-42909520	HCT-116	colon:	n/a	n/a
5	ZMIZ1	chr5:42908966-42909361	K562	blood:	n/a	n/a
6	RAD21	chr5:42909045-42909355	SK-N-SH_RA	brain:	n/a	n/a
7	RAD21	chr5:42908919-42909536	A549	lung:	n/a	n/a
8	CTCF	chr5:42909055-42909307	A549	lung:	n/a	n/a
9	RAD21	chr5:42908954-42909399	A549	lung:	n/a	n/a
10	RAD21	chr5:42908678-42909411	H1-hESC	embryonic stem cell:	n/a	n/a
11	ARID3A	chr5:42908844-42909308	K562	blood:	n/a	n/a
12	PML	chr5:42908704-42909330	GM12878	blood:	n/a	n/a
13	CTCF	chr5:42908960-42909321	HepG2	liver:	n/a	n/a
14	YY1	chr5:42908969-42909321	GM12878	blood:	n/a	n/a
15	GTF2F1	chr5:42909024-42909386	Hela-S3	cervix:	n/a	n/a
16	MTA3	chr5:42908539-42909442	GM12878	blood:	n/a	n/a
17	CTCF	chr5:42908925-42909387	K562	blood:	n/a	n/a
18	CTCF	chr5:42909046-42909324	MCF-7	breast:	n/a	n/a
19	CTCF	chr5:42909049-42909317	SK-N-SH_RA	brain:	n/a	n/a
20	CTCF	chr5:42908975-42909361	A549	lung:	n/a	n/a
21	POLR2A	chr5:42908847-42909334	PANC-1	pancreas:	n/a	n/a
22	CTCF	chr5:42909027-42909308	HUVEC	blood vessel:	n/a	n/a
23	PAX5	chr5:42909012-42909339	GM12878	blood:	n/a	n/a
24	CTCF	chr5:42909036-42909329	K562	blood:	n/a	n/a
25	CTCF	chr5:42909140-42909290	BE2_C	brain:	n/a	n/a
26	RAD21	chr5:42909052-42909372	GM12878	blood:	n/a	n/a
27	CTCF	chr5:42909021-42909339	A549	lung:	n/a	n/a
28	RAD21	chr5:42908997-42909436	HepG2	liver:	n/a	n/a
29	CHD2	chr5:42908975-42909339	GM12878	blood:	n/a	n/a
30	CTCF	chr5:42908941-42909384	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr5:42908777-42909306	Hela-S3	cervix:	n/a	n/a
32	ZBTB7A	chr5:42909086-42909456	K562	blood:	n/a	n/a
33	RAD21	chr5:42908679-42909502	IMR90	lung:	n/a	n/a
34	CTCF	chr5:42909032-42909300	Pancreas_OC	pancreas:	n/a	n/a
35	CTCF	chr5:42909046-42909325	MCF-7	breast:	n/a	n/a
36	WRNIP1	chr5:42908950-42909362	GM12878	blood:	n/a	n/a
37	RCOR1	chr5:42908679-42909352	K562	blood:	n/a	n/a
38	CTCF	chr5:42909017-42909338	GM12878	blood:	n/a	n/a
39	MAX	chr5:42908671-42909297	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr5:42908976-42909384	MCF-7	breast:	n/a	n/a
41	CTCF	chr5:42908918-42909447	GM12878	blood:	n/a	n/a
42	ZNF143	chr5:42908583-42909333	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr5:42908931-42909379	ECC-1	luminal epithelium:	n/a	n/a
44	NRF1	chr5:42908557-42909430	SK-N-SH	brain:	n/a	chr5:42908869-42908883 chr5:42909110-42909121
45	FOS	chr5:42909154-42909331	MCF10A-Er-Src	breast:	n/a	n/a
46	SMC3	chr5:42908893-42909400	Hela-S3	cervix:	n/a	n/a
47	SMC3	chr5:42908586-42909478	SK-N-SH	brain:	n/a	n/a
48	CTCF	chr5:42909029-42909310	MCF-7	breast:	n/a	n/a
49	CTCF	chr5:42909008-42909316	ECC-1	luminal epithelium:	n/a	n/a
50	CTCF	chr5:42909038-42909324	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:42908857..42910740-chr5:43065280..43068531,3	K562	blood:
2	chr5:42909069..42910039-chr5:43389624..43390382,2	MCF-7	breast:
3	chr5:42909164..42909729-chr5:43039167..43040032,2	K562	blood:
4	chr5:42907363..42912501-chr5:43064737..43069149,8	MCF-7	breast:
5	chr5:42908654..42910895-chr5:43006900..43010047,5	MCF-7	breast:
6	chr5:42908870..42911135-chr5:43009033..43010803,2	K562	blood:
7	chr5:42908849..42909564-chr5:43064584..43065395,2	K562	blood:
8	chr5:42909052..42909674-chr5:43039401..43040103,2	MCF-7	breast:
9	chr5:42907010..42910562-chr5:43064999..43067630,3	MCF-7	breast:
10	chr5:42907581..42909848-chr5:43040254..43042169,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000251656	TF binding region
ENSG00000215068	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000177738	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10036147	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10036468	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10044301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053947	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061198	0.98[ASN][1000 genomes]
rs10068961	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072017	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12655096	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12658770	0.95[ASN][1000 genomes]
rs12659760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354920	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160330	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs188793	0.93[CEU][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1902100	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098715	0.91[ASN][1000 genomes]
rs2548362	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548364	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548365	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2548366	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2603622	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603624	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28415991	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309932	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309934	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309935	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309942	0.89[EUR][1000 genomes]
rs315246	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315253	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315263	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34917335	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34981544	0.98[ASN][1000 genomes]
rs371261	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs378235	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs378344	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs388214	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs420550	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs435312	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs446294	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4482913	0.98[ASN][1000 genomes]
rs453436	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451649	0.98[ASN][1000 genomes]
rs6451650	0.98[ASN][1000 genomes]
rs6451651	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6451652	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6451653	0.91[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs6451654	0.90[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs6864892	0.91[ASN][1000 genomes]
rs6867854	0.94[ASN][1000 genomes]
rs6875237	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6881608	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6885355	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6886626	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6895458	0.98[ASN][1000 genomes]
rs6895751	0.98[ASN][1000 genomes]
rs71627562	0.92[ASN][1000 genomes]
rs71627563	0.92[ASN][1000 genomes]
rs7701142	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7721545	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9885101	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
7	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
8	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv980936	chr5:42894375-42930741	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv968909	chr5:42903982-42953465	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1806082	chr5:42906572-42967215	Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42908400-42909400	Flanking Active TSS	Liver	Liver
2	chr5:42908400-42909400	Active TSS	Brain Hippocampus Middle	brain
3	chr5:42908400-42909400	Flanking Active TSS	K562	blood
4	chr5:42908600-42909400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:42908600-42909400	Bivalent/Poised TSS	Fetal Brain Female	brain
6	chr5:42908600-42909400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr5:42908800-42909400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr5:42908800-42909400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr5:42908800-42909400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:42908800-42909400	Active TSS	A549	lung
11	chr5:42908800-42909600	Active TSS	Brain Anterior Caudate	brain
12	chr5:42909000-42909400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:42909000-42909400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:42909000-42909400	Active TSS	Brain Angular Gyrus	brain
15	chr5:42909000-42909400	Active TSS	Colonic Mucosa	Colon
16	chr5:42909000-42909400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr5:42909000-42909400	Active TSS	Stomach Smooth Muscle	stomach
18	chr5:42909000-42909400	Flanking Active TSS	Dnd41	blood
19	chr5:42909000-42909400	Flanking Active TSS	Hela-S3	cervix
20	chr5:42909000-42909400	Active TSS	Osteobl	bone
21	chr5:42909000-42910000	Active TSS	HepG2	liver
22	chr5:42909200-42909400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:42909200-42909400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:42909200-42909400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:42909200-42909400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:42909200-42909400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:42909200-42909400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:42909200-42909400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr5:42909200-42909400	Enhancers	Primary B cells from peripheral blood	blood
30	chr5:42909200-42909400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr5:42909200-42909400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr5:42909200-42909400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:42909200-42909400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:42909200-42909400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr5:42909200-42909400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:42909200-42909400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:42909200-42909400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr5:42909200-42909400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr5:42909200-42909400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:42909200-42909400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:42909200-42909400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:42909200-42909400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr5:42909200-42909400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:42909200-42909400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:42909200-42909400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:42909200-42909400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:42909200-42909400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:42909200-42909400	Enhancers	Adipose Nuclei	Adipose
49	chr5:42909200-42909400	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr5:42909200-42909400	Bivalent Enhancer	Brain Germinal Matrix	brain

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