Variant report

Variant	rs57236484
Chromosome Location	chr3:52091770-52091771
allele	A/G
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	HEY1	chr3:52091481-52091885	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52090932-52091951	U87	brain:	n/a	n/a
3	RAD21	chr3:52091415-52091799	HepG2	liver:	n/a	chr3:52091686-52091700
4	RUNX3	chr3:52090568-52091830	GM12878	blood:	n/a	n/a
5	MAX	chr3:52091092-52091824	HepG2	liver:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
6	MAZ	chr3:52090543-52091787	Hela-S3	cervix:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
7	BHLHE40	chr3:52091060-52091780	GM12878	blood:	n/a	chr3:52091498-52091514
8	MAZ	chr3:52088560-52092528	IMR90	lung:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
9	POLR2A	chr3:52090426-52091951	H1-neurons	neurons:	n/a	n/a
10	REST	chr3:52089552-52092345	H1-neurons	neurons:	n/a	chr3:52091575-52091588 chr3:52091918-52091931 chr3:52091489-52091502
11	POLR2A	chr3:52090938-52091899	U87	brain:	n/a	n/a
12	CTCF	chr3:52091208-52091776	GM12878	blood:	n/a	chr3:52091657-52091665
13	CTCF	chr3:52091700-52091850	HRE	kidney:	n/a	n/a
14	CHD2	chr3:52090566-52091794	Hela-S3	cervix:	n/a	chr3:52090988-52090998 chr3:52090658-52090665
15	POLR2A	chr3:52090456-52091803	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr3:52089731-52091776	K562	blood:	n/a	n/a
17	HA-E2F1	chr3:52090611-52091850	MCF-7	breast:	n/a	chr3:52091635-52091645 chr3:52091822-52091831 chr3:52091442-52091452 chr3:52090658-52090665 chr3:52091638-52091647 chr3:52091523-52091535 chr3:52091495-52091504
18	MAZ	chr3:52090460-52091867	GM12878	blood:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
19	NRF1	chr3:52090395-52092278	SK-N-SH	brain:	n/a	chr3:52091535-52091544 chr3:52090837-52090851 chr3:52091546-52091555 chr3:52091643-52091657 chr3:52091575-52091584
20	RCOR1	chr3:52091079-52091784	HepG2	liver:	n/a	n/a
21	CREB1	chr3:52091014-52091831	GM12878	blood:	n/a	n/a
22	E2F4	chr3:52091098-52091785	MCF10A-Er-Src	breast:	n/a	chr3:52091635-52091645 chr3:52091442-52091452 chr3:52091638-52091647 chr3:52091523-52091535 chr3:52091495-52091504
23	POLR2A	chr3:52091538-52091815	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:52091509-52091850	ECC-1	luminal epithelium:	n/a	n/a
25	TAF1	chr3:52091443-52091834	HepG2	liver:	n/a	n/a
26	BACH1	chr3:52090669-52092031	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr3:52090445-52091921	HCT-116	colon:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
28	CREB1	chr3:52090810-52091839	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:52091383-52091851	Hela-S3	cervix:	n/a	n/a
30	SP1	chr3:52090462-52091770	A549	lung:	n/a	chr3:52091496-52091505 chr3:52091494-52091506 chr3:52091535-52091545 chr3:52091399-52091413 chr3:52091534-52091546 chr3:52091534-52091546 chr3:52091535-52091544 chr3:52090948-52090957 chr3:52090678-52090687 chr3:52091531-52091545 chr3:52091494-52091506 chr3:52091495-52091504 chr3:52091417-52091438 chr3:52090947-52090957 chr3:52091536-52091545 chr3:52091491-52091505 chr3:52091535-52091545
31	USF1	chr3:52090920-52091773	HCT-116	colon:	n/a	chr3:52091498-52091514 chr3:52091335-52091346
32	HCFC1	chr3:52090458-52092025	Hela-S3	cervix:	n/a	n/a
33	MAX	chr3:52089605-52091926	ECC-1	luminal epithelium:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
34	MAX	chr3:52090508-52091948	HepG2	liver:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
35	CHD2	chr3:52090621-52091791	GM12878	blood:	n/a	chr3:52090988-52090998 chr3:52090658-52090665
36	POLR2A	chr3:52091491-52091782	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:52091308-52092071	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:52091087-52091836	GM15510	blood:	n/a	n/a
39	POLR2A	chr3:52091555-52091818	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:52091185-52091835	HUVEC	blood vessel:	n/a	n/a
41	SP1	chr3:52091095-52091848	GM12878	blood:	n/a	chr3:52091496-52091505 chr3:52091494-52091506 chr3:52091535-52091545 chr3:52091399-52091413 chr3:52091534-52091546 chr3:52091534-52091546 chr3:52091535-52091544 chr3:52091531-52091545 chr3:52091494-52091506 chr3:52091495-52091504 chr3:52091417-52091438 chr3:52091536-52091545 chr3:52091491-52091505 chr3:52091535-52091545
42	MAZ	chr3:52090472-52091819	K562	blood:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
43	MAX	chr3:52089267-52091929	A549	lung:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
44	NFYB	chr3:52091122-52091793	K562	blood:	n/a	chr3:52091413-52091428
45	SP4	chr3:52091155-52091777	H1-hESC	embryonic stem cell:	n/a	chr3:52091530-52091546 chr3:52091532-52091548
46	POLR2A	chr3:52089093-52091883	Hela-S3	cervix:	n/a	n/a
47	ZNF143	chr3:52090883-52092053	H1-hESC	embryonic stem cell:	n/a	chr3:52091575-52091593 chr3:52091545-52091555
48	MXI1	chr3:52089200-52091794	IMR90	lung:	n/a	chr3:52091337-52091346
49	MAX	chr3:52089607-52091992	HepG2	liver:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
50	MAX	chr3:52090509-52091890	ECC-1	luminal epithelium:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346

No.	Distal block	Cell Line	Cell type
1	chr3:52028061..52031321-chr3:52088873..52092735,5	MCF-7	breast:
2	chr3:52091359..52093112-chr3:52104568..52106950,2	K562	blood:
3	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:
4	chr3:52015921..52019600-chr3:52088214..52092499,4	K562	blood:

Variant related genes	Relation type
DUSP7	TF binding region
ENSG00000243989	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000256097	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10433611	1.00[AMR][1000 genomes]
rs2089225	1.00[AMR][1000 genomes]
rs323888	1.00[AMR][1000 genomes]
rs323899	1.00[AMR][1000 genomes]
rs323901	1.00[AMR][1000 genomes]
rs352646	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35898691	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59196507	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61333587	1.00[AMR][1000 genomes]
rs6446153	1.00[AMR][1000 genomes]
rs72955239	1.00[AMR][1000 genomes]
rs72955243	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955259	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955260	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955262	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7430706	1.00[AMR][1000 genomes]
rs7612847	1.00[AMR][1000 genomes]

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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	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
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	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
11	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv590282	chr3:52088204-52097060	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv1836489	chr3:52089837-52101799	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv1838771	chr3:52089837-52101799	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv590293	chr3:52089889-52097060	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv590299	chr3:52090344-52096432	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv590300	chr3:52090597-52096432	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52087400-52091800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52088600-52091800	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr3:52088600-52091800	Active TSS	Aorta	Aorta
4	chr3:52088600-52092000	Active TSS	Fetal Kidney	kidney
5	chr3:52088600-52092000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:52088800-52091800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52088800-52091800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:52088800-52091800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:52088800-52091800	Active TSS	Ovary	ovary
10	chr3:52088800-52091800	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr3:52088800-52091800	Active TSS	Small Intestine	intestine
12	chr3:52089000-52091800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr3:52089000-52091800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:52089000-52091800	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:52089000-52091800	Active TSS	Left Ventricle	heart
16	chr3:52089000-52092000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:52089000-52092000	Active TSS	A549	lung
18	chr3:52089200-52091800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:52089400-52091800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:52089800-52091800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:52090000-52091800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:52090000-52091800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:52090200-52091800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:52090200-52091800	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:52090200-52091800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:52090200-52091800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:52090600-52092000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:52090600-52092000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:52090600-52092200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:52090600-52092200	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr3:52090800-52092000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr3:52090800-52092000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:52090800-52092000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr3:52090800-52092000	Flanking Active TSS	Dnd41	blood
35	chr3:52090800-52092200	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr3:52091200-52091800	Active TSS	Primary T cells from cord blood	blood
37	chr3:52091200-52091800	Active TSS	Brain Cingulate Gyrus	brain
38	chr3:52091200-52091800	Active TSS	Brain Germinal Matrix	brain
39	chr3:52091200-52091800	Active TSS	Brain Hippocampus Middle	brain
40	chr3:52091200-52091800	Active TSS	Fetal Brain Female	brain
41	chr3:52091200-52091800	Active TSS	Right Ventricle	heart
42	chr3:52091200-52092000	Active TSS	Right Atrium	heart
43	chr3:52091200-52092400	Enhancers	Fetal Heart	heart
44	chr3:52091200-52092600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:52091200-52092800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:52091400-52092400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:52091400-52092400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:52091400-52092600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:52091600-52091800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:52091600-52091800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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