Variant report

Variant	rs547246223
Chromosome Location	chr3:52091287-52091288
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	FOS	chr3:52091180-52091585	MCF10A-Er-Src	breast:	n/a	chr3:52091494-52091503
2	MTA3	chr3:52090616-52091430	GM12878	blood:	n/a	n/a
3	SIN3A	chr3:52090567-52091511	GM12878	blood:	n/a	chr3:52091337-52091346
4	SIN3AK20	chr3:52091133-52091417	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:52090932-52091951	U87	brain:	n/a	n/a
6	POLR2A	chr3:52091057-52091648	IMR90	lung:	n/a	n/a
7	SP2	chr3:52091152-52091679	HepG2	liver:	n/a	chr3:52091398-52091413
8	TBP	chr3:52090932-52091712	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:52090438-52091336	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr3:52090527-52091497	H1-hESC	embryonic stem cell:	n/a	n/a
11	RUNX3	chr3:52090568-52091830	GM12878	blood:	n/a	n/a
12	MAX	chr3:52090731-52091526	A549	lung:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
13	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
14	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
15	EP300	chr3:52090636-52091473	K562	blood:	n/a	n/a
16	BHLHE40	chr3:52091060-52091780	GM12878	blood:	n/a	chr3:52091498-52091514
17	NFYA	chr3:52091190-52091617	GM12878	blood:	n/a	chr3:52091416-52091434
18	SP2	chr3:52091142-52091639	HepG2	liver:	n/a	chr3:52091398-52091413
19	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
20	POLR2A	chr3:52090426-52091951	H1-neurons	neurons:	n/a	n/a
21	REST	chr3:52089552-52092345	H1-neurons	neurons:	n/a	chr3:52091575-52091588 chr3:52091918-52091931 chr3:52091489-52091502
22	RCOR1	chr3:52090612-52091688	K562	blood:	n/a	n/a
23	POLR2A	chr3:52090938-52091899	U87	brain:	n/a	n/a
24	SP2	chr3:52091169-52091652	H1-hESC	embryonic stem cell:	n/a	chr3:52091398-52091413
25	RFX5	chr3:52091104-52091711	Hela-S3	cervix:	n/a	n/a
26	TEAD4	chr3:52090820-52091506	K562	blood:	n/a	n/a
27	CTCF	chr3:52091217-52091408	Lung_OC	lung:	n/a	n/a
28	CTCF	chr3:52091208-52091776	GM12878	blood:	n/a	chr3:52091657-52091665
29	USF1	chr3:52091083-52091570	A549	lung:	n/a	chr3:52091498-52091514 chr3:52091335-52091346
30	EP300	chr3:52091129-52091649	HepG2	liver:	n/a	chr3:52091500-52091509
31	TBP	chr3:52091133-52091727	K562	blood:	n/a	n/a
32	POLR2A	chr3:52091253-52091711	HUVEC	blood vessel:	n/a	n/a
33	USF1	chr3:52090970-52091734	ECC-1	luminal epithelium:	n/a	chr3:52091498-52091514 chr3:52091335-52091346
34	CHD2	chr3:52090566-52091794	Hela-S3	cervix:	n/a	chr3:52090988-52090998 chr3:52090658-52090665
35	POLR2A	chr3:52090008-52091698	NB4	blood:	n/a	n/a
36	MYC	chr3:52089257-52091661	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
37	TBL1XR1	chr3:52090576-52091691	GM12878	blood:	n/a	n/a
38	CHD2	chr3:52091241-52091652	K562	blood:	n/a	n/a
39	YY1	chr3:52091202-52091605	HCT-116	colon:	n/a	chr3:52091575-52091589 chr3:52091498-52091512 chr3:52091581-52091592
40	USF2	chr3:52091150-52091513	K562	blood:	n/a	chr3:52091335-52091346
41	MYC	chr3:52089648-52091728	NB4	blood:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
42	BHLHE40	chr3:52090568-52091738	K562	blood:	n/a	chr3:52091498-52091514 chr3:52090590-52090606
43	POLR2A	chr3:52090456-52091803	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr3:52089731-52091776	K562	blood:	n/a	n/a
45	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
46	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
47	MAFK	chr3:52091121-52091654	Hela-S3	cervix:	n/a	n/a
48	RCOR1	chr3:52090738-52091397	K562	blood:	n/a	n/a
49	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
50	CHD2	chr3:52090894-52091692	H1-hESC	embryonic stem cell:	n/a	chr3:52090988-52090998

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52091282-52091332	CMK	blood:	n/a
2	chr3:52091282-52091332	H1-hESC	embryonic stem cell:	embryo
3	chr3:52091282-52091332	AG10803	skin:	n/a
4	chr3:52091282-52091332	HMEC	breast:	n/a
5	chr3:52091282-52091332	GM06990	blood:	n/a
6	chr3:52091282-52091332	NT2-D1	testis:	n/a
7	chr3:52091282-52091332	ECC-1	luminal epithelium:	n/a
8	chr3:52091282-52091332	T-47D	breast:	n/a
9	chr3:52091282-52091332	GM12891	blood:	n/a
10	chr3:52091282-52091332	BJ	skin:	n/a
11	chr3:52091282-52091332	HEEpiC	esophagus:	n/a
12	chr3:52091282-52091332	Caco-2	colon:	n/a
13	chr3:52091282-52091332	SK-N-MC	brain:	n/a
14	chr3:52091282-52091332	SAEC	small airway:	n/a
15	chr3:52091282-52091332	HUVEC	blood vessel:	n/a
16	chr3:52091282-52091332	MCF10A-Er-Src	breast:	n/a
17	chr3:52091282-52091332	SK-N-SH	brain:	n/a
18	chr3:52091282-52091332	BE2_C	brain:	n/a
19	chr3:52091282-52091332	HL-60	blood:	n/a
20	chr3:52091282-52091332	PrEC	prostate:	n/a
21	chr3:52091282-52091332	NHBE	bronchial:	n/a
22	chr3:52091282-52091332	HRE	kidney:	n/a
23	chr3:52091282-52091332	LNCaP	prostate:	n/a
24	chr3:52091282-52091332	Jurkat	blood:	n/a
25	chr3:52091282-52091332	HCM	heart:	n/a
26	chr3:52091282-52091332	HCF	heart:	n/a
27	chr3:52091282-52091332	HRPEpiC	eye:	n/a
28	chr3:52091282-52091332	GM19239	blood:	n/a
29	chr3:52091282-52091332	RPTEC	kidney:	n/a
30	chr3:52091282-52091332	IMR90	lung:	fetal
31	chr3:52091282-52091332	PANC-1	pancreas:	n/a
32	chr3:52091282-52091332	AoSMC	blood vessel:	n/a
33	chr3:52091282-52091332	K562	blood:	n/a
34	chr3:52091282-52091332	GM12892	blood:	n/a
35	chr3:52091282-52091332	NH-A	brain:	n/a
36	chr3:52091282-52091332	Hepatocyte	liver:	n/a
37	chr3:52091282-52091332	AG09319	gingival:	n/a
38	chr3:52091282-52091332	HCPEpiC	choroid plexus:	n/a
39	chr3:52091282-52091332	MCF-7	breast:	n/a
40	chr3:52091282-52091332	Hela-S3	cervix:	n/a
41	chr3:52091282-52091332	HIPEpiC	eye:	n/a
42	chr3:52091282-52091332	ProgFib	skin:	n/a
43	chr3:52091282-52091332	HAEpiC	amniotic membrane:	n/a
44	chr3:52091282-52091332	HPAEpiC	pulmonary alveolar:	n/a
45	chr3:52091282-52091332	GM12878	blood:	n/a
46	chr3:52091282-52091332	ovcar-3	ovarian:	n/a
47	chr3:52091282-52091332	SKMC	muscle:	n/a
48	chr3:52091282-52091332	AG09309	skin:	n/a
49	chr3:52091282-52091332	HepG2	liver:	n/a
50	chr3:52091282-52091332	HCT-116	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52016320..52018909-chr3:52089400..52091632,2	MCF-7	breast:
2	chr1:149222699..149225112-chr3:52088904..52091700,2	MCF-7	breast:
3	chr3:52089814..52091351-chr3:52187528..52189873,2	K562	blood:
4	chr3:52028061..52031321-chr3:52088873..52092735,5	MCF-7	breast:
5	chr3:52026823..52031380-chr3:52087204..52091486,4	K562	blood:
6	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:
7	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:
8	chr3:52015921..52019600-chr3:52088214..52092499,4	K562	blood:
9	chr3:51975919..51976628-chr3:52090698..52091583,2	K562	blood:

Variant related genes	Relation type
DUSP7	TF binding region
DUSP7	CpG island
ENSG00000162244	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000256097	Chromatin interaction
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:19 , 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	esv3355709	chr3:52088937-52091485	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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:127 , 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	chr3:52088600-52091600	Active TSS	Psoas Muscle	Psoas
3	chr3:52088600-52091800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr3:52088600-52091800	Active TSS	Aorta	Aorta
5	chr3:52088600-52092000	Active TSS	Fetal Kidney	kidney
6	chr3:52088600-52092000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:52088800-52091400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:52088800-52091600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:52088800-52091600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:52088800-52091600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:52088800-52091600	Active TSS	Brain Substantia Nigra	brain
12	chr3:52088800-52091600	Active TSS	Gastric	stomach
13	chr3:52088800-52091600	Active TSS	Lung	lung
14	chr3:52088800-52091600	Active TSS	Osteobl	bone
15	chr3:52088800-52091800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52088800-52091800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:52088800-52091800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr3:52088800-52091800	Active TSS	Ovary	ovary
19	chr3:52088800-52091800	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr3:52088800-52091800	Active TSS	Small Intestine	intestine
21	chr3:52089000-52091600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:52089000-52091600	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr3:52089000-52091600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:52089000-52091600	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr3:52089000-52091600	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:52089000-52091600	Active TSS	Duodenum Mucosa	Duodenum
27	chr3:52089000-52091600	Active TSS	HSMMtube	muscle
28	chr3:52089000-52091600	Active TSS	K562	blood
29	chr3:52089000-52091800	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:52089000-52091800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:52089000-52091800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr3:52089000-52091800	Active TSS	Left Ventricle	heart
33	chr3:52089000-52092000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:52089000-52092000	Active TSS	A549	lung
35	chr3:52089200-52091800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:52089400-52091800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr3:52089600-52091600	Active TSS	Placenta Amnion	Placenta Amnion
38	chr3:52089600-52091600	Active TSS	Thymus	Thymus
39	chr3:52089800-52091600	Active TSS	NHEK	skin
40	chr3:52089800-52091800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:52090000-52091600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:52090000-52091800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr3:52090000-52091800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:52090200-52091400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:52090200-52091800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:52090200-52091800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:52090200-52091800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:52090200-52091800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:52090600-52091400	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:52090600-52091400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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