Variant report

Variant	rs533931712
Chromosome Location	chr3:178789534-178789535
allele	C/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	ZNF143	chr3:178788908-178790072	GM12878	blood:	n/a	chr3:178789152-178789170
2	POLR2A	chr3:178788718-178790508	GM12878	blood:	n/a	n/a
3	JUND	chr3:178789181-178789934	H1-hESC	embryonic stem cell:	n/a	chr3:178789723-178789732
4	ELF1	chr3:178789318-178790210	HepG2	liver:	n/a	chr3:178789678-178789687 chr3:178790046-178790059 chr3:178789504-178789516
5	TAF1	chr3:178789402-178789824	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:178789514-178789808	A549	lung:	n/a	n/a
7	POLR2A	chr3:178789292-178789944	A549	lung:	n/a	n/a
8	ELK1	chr3:178789217-178790201	GM12878	blood:	n/a	n/a
9	ZNF143	chr3:178789235-178789726	K562	blood:	n/a	n/a
10	POLR2A	chr3:178788597-178790407	GM18505	blood:	n/a	n/a
11	POLR2A	chr3:178789436-178789875	A549	lung:	n/a	n/a
12	TAF1	chr3:178789281-178789892	K562	blood:	n/a	n/a
13	JUND	chr3:178788802-178790289	K562	blood:	n/a	chr3:178789723-178789732
14	MAX	chr3:178788899-178790200	HepG2	liver:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
15	POLR2A	chr3:178789286-178790065	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr3:178789381-178789871	SK-N-SH	brain:	n/a	n/a
17	MXI1	chr3:178787729-178790159	IMR90	lung:	n/a	n/a
18	NFATC1	chr3:178788862-178790387	GM12878	blood:	n/a	n/a
19	MAX	chr3:178788868-178790192	HCT-116	colon:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
20	POLR2A	chr3:178789266-178790383	K562	blood:	n/a	n/a
21	POLR2A	chr3:178789090-178790361	K562	blood:	n/a	n/a
22	POLR2A	chr3:178788869-178790435	GM12891	blood:	n/a	n/a
23	JUND	chr3:178789390-178789897	A549	lung:	n/a	chr3:178789723-178789732
24	POLR2A	chr3:178789288-178790064	Hela-S3	cervix:	n/a	n/a
25	TCF7L2	chr3:178789082-178789980	HCT-116	colon:	n/a	chr3:178789788-178789798
26	ELF1	chr3:178789468-178789710	A549	lung:	n/a	chr3:178789678-178789687 chr3:178789504-178789516
27	MAX	chr3:178788878-178790157	ECC-1	luminal epithelium:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
28	POLR2A	chr3:178788832-178790483	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:178788999-178789905	HepG2	liver:	n/a	n/a
30	HEY1	chr3:178789306-178789943	HepG2	liver:	n/a	chr3:178789506-178789521
31	GABPA	chr3:178789008-178790022	SK-N-SH	brain:	n/a	chr3:178789654-178789665 chr3:178789654-178789663 chr3:178789724-178789733 chr3:178789765-178789774 chr3:178789651-178789665
32	E2F1	chr3:178789124-178789862	Hela-S3	cervix:	n/a	chr3:178789655-178789664
33	POLR2A	chr3:178788899-178790390	GM12891	blood:	n/a	n/a
34	POLR2A	chr3:178788918-178790493	GM19193	blood:	n/a	n/a
35	POLR2A	chr3:178788980-178790289	GM15510	blood:	n/a	n/a
36	POLR2A	chr3:178788923-178790330	GM18526	blood:	n/a	n/a
37	NRF1	chr3:178789468-178789810	Hela-S3	cervix:	n/a	chr3:178789653-178789664 chr3:178789654-178789665 chr3:178789654-178789663 chr3:178789724-178789733 chr3:178789765-178789774 chr3:178789631-178789642 chr3:178789651-178789665
38	YY1	chr3:178789423-178789827	A549	lung:	n/a	chr3:178789503-178789517 chr3:178789508-178789517
39	NRF1	chr3:178789472-178789851	H1-hESC	embryonic stem cell:	n/a	chr3:178789653-178789664 chr3:178789654-178789665 chr3:178789654-178789663 chr3:178789724-178789733 chr3:178789765-178789774 chr3:178789631-178789642 chr3:178789651-178789665
40	POLR2A	chr3:178789275-178789999	ECC-1	luminal epithelium:	n/a	n/a
41	POU2F2	chr3:178788892-178789898	GM12891	blood:	n/a	chr3:178789521-178789533
42	TCF3	chr3:178789371-178789751	GM12878	blood:	n/a	chr3:178789575-178789589
43	POLR2A	chr3:178788908-178790352	GM18951	blood:	n/a	n/a
44	USF2	chr3:178789025-178790057	GM12878	blood:	n/a	chr3:178789275-178789286 chr3:178789680-178789696 chr3:178789719-178789735
45	POLR2A	chr3:178789421-178789934	K562	blood:	n/a	n/a
46	NRF1	chr3:178789475-178789798	HepG2	liver:	n/a	chr3:178789653-178789664 chr3:178789654-178789665 chr3:178789654-178789663 chr3:178789724-178789733 chr3:178789765-178789774 chr3:178789631-178789642 chr3:178789651-178789665
47	POLR2A	chr3:178789445-178789835	H1-hESC	embryonic stem cell:	n/a	n/a
48	TBL1XR1	chr3:178788901-178790105	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:178788967-178790444	GM12892	blood:	n/a	n/a
50	SIN3AK20	chr3:178789097-178789717	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:178789534-178789584	AG09309	skin:	n/a
2	chr3:178789528-178789578	GM19239	blood:	n/a
3	chr3:178789534-178789584	GM12878	blood:	n/a
4	chr3:178789528-178789578	IMR90	lung:	fetal
5	chr3:178789534-178789584	A549	lung:	n/a
6	chr3:178789534-178789584	NH-A	brain:	n/a
7	chr3:178789528-178789578	SK-N-SH_RA	brain:	n/a
8	chr3:178789534-178789584	HMEC	breast:	n/a
9	chr3:178789528-178789578	MCF10A-Er-Src	breast:	n/a
10	chr3:178789534-178789584	SK-N-SH	brain:	n/a
11	chr3:178789528-178789578	HRCEpiC	kidney:	n/a
12	chr3:178789528-178789578	NH-A	brain:	n/a
13	chr3:178789528-178789578	HL-60	blood:	n/a
14	chr3:178789528-178789578	PFSK-1	brain:	n/a
15	chr3:178789534-178789584	IMR90	lung:	fetal
16	chr3:178789534-178789584	HUVEC	blood vessel:	n/a
17	chr3:178789528-178789578	AG09309	skin:	n/a
18	chr3:178789534-178789584	GM19239	blood:	n/a
19	chr3:178789528-178789578	Hepatocyte	liver:	n/a
20	chr3:178789534-178789584	HCM	heart:	n/a
21	chr3:178789528-178789578	HRE	kidney:	n/a
22	chr3:178789534-178789584	AG04449	skin:	fetal
23	chr3:178789528-178789578	HEEpiC	esophagus:	n/a
24	chr3:178789528-178789578	HCPEpiC	choroid plexus:	n/a
25	chr3:178789534-178789584	NT2-D1	testis:	n/a
26	chr3:178789528-178789578	SKMC	muscle:	n/a
27	chr3:178789528-178789578	HMEC	breast:	n/a
28	chr3:178789528-178789578	GM12878	blood:	n/a
29	chr3:178789534-178789584	ECC-1	luminal epithelium:	n/a
30	chr3:178789534-178789584	MCF-7	breast:	n/a
31	chr3:178789534-178789584	GM12892	blood:	n/a
32	chr3:178789528-178789578	HepG2	liver:	n/a
33	chr3:178789534-178789584	ovcar-3	ovarian:	n/a
34	chr3:178789534-178789584	HRE	kidney:	n/a
35	chr3:178789534-178789584	NHDF-neo	bronchial:	n/a
36	chr3:178789534-178789584	AG04450	lung:	fetal
37	chr3:178789528-178789578	HCF	heart:	n/a
38	chr3:178789534-178789584	Jurkat	blood:	n/a
39	chr3:178789528-178789578	GM12892	blood:	n/a
40	chr3:178789528-178789578	HNPCEpiC	eye:	n/a
41	chr3:178789534-178789584	HPAEpiC	pulmonary alveolar:	n/a
42	chr3:178789528-178789578	ovcar-3	ovarian:	n/a
43	chr3:178789534-178789584	LNCaP	prostate:	n/a
44	chr3:178789528-178789578	NB4	blood:	n/a
45	chr3:178789528-178789578	NHBE	bronchial:	n/a
46	chr3:178789534-178789584	SK-N-MC	brain:	n/a
47	chr3:178789534-178789584	HEK293	kidney:	embryo
48	chr3:178789534-178789584	Hela-S3	cervix:	n/a
49	chr3:178789534-178789584	T-47D	breast:	n/a
50	chr3:178789528-178789578	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:178788412..178790187-chr3:179039067..179041157,2	MCF-7	breast:
2	chr3:178787120..178791261-chr3:179039253..179041998,3	K562	blood:
3	chr3:178788594..178790647-chr3:179063924..179066564,2	K562	blood:
4	chr3:178787966..178791118-chr3:178865051..178866959,3	MCF-7	breast:
5	chr3:178787639..178789990-chr3:179064273..179066880,2	MCF-7	breast:
6	chr3:178788554..178791044-chr3:178814072..178816691,3	MCF-7	breast:
7	chr3:178786925..178790579-chr3:178864297..178867679,5	K562	blood:
8	chr3:178788447..178791036-chr3:178864497..178866649,2	MCF-7	breast:
9	chr3:178787618..178789818-chr3:179039518..179042108,2	K562	blood:
10	chr3:178787982..178790546-chr3:179037129..179041546,5	MCF-7	breast:
11	chr3:178787758..178789707-chr3:178977770..178980269,2	MCF-7	breast:

Variant related genes	Relation type
ZMAT3	TF binding region
ZMAT3	CpG island
ENSG00000200616	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000240429	Chromatin interaction
ENSG00000171109	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000121879	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3325944	chr3:178788483-178791031	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178785600-178790000	Active TSS	GM12878-XiMat	blood
2	chr3:178786600-178790200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:178786800-178789800	Active TSS	NH-A	brain
4	chr3:178787000-178789600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:178787000-178789800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:178787000-178789800	Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr3:178787000-178790000	Active TSS	NHDF-Ad	bronchial
8	chr3:178787000-178790200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:178787000-178790200	Active TSS	HSMMtube	muscle
10	chr3:178787000-178790400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:178787200-178789800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:178787200-178790200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:178787200-178790200	Active TSS	NHLF	lung
14	chr3:178787200-178790400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:178787400-178789800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:178787400-178789800	Active TSS	HMEC	breast
17	chr3:178787400-178790000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:178787400-178790200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:178787400-178790200	Active TSS	Thymus	Thymus
20	chr3:178787400-178790400	Active TSS	A549	lung
21	chr3:178787600-178789800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:178787600-178789800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr3:178787600-178789800	Active TSS	HSMM	muscle
24	chr3:178787600-178790200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:178787600-178790400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:178787800-178790200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:178787800-178790200	Active TSS	Aorta	Aorta
28	chr3:178787800-178790200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:178787800-178790400	Active TSS	Brain Hippocampus Middle	brain
30	chr3:178788000-178790400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:178788000-178790400	Active TSS	Brain Substantia Nigra	brain
32	chr3:178788200-178790400	Active TSS	Brain Cingulate Gyrus	brain
33	chr3:178788200-178790400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr3:178788400-178789800	Active TSS	H1 Cell Line	embryonic stem cell
35	chr3:178788400-178789800	Active TSS	Fetal Lung	lung
36	chr3:178788400-178790000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:178788400-178790000	Active TSS	Stomach Mucosa	stomach
38	chr3:178788400-178790200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr3:178788400-178790200	Active TSS	Rectal Smooth Muscle	rectum
40	chr3:178788400-178790400	Active TSS	Colonic Mucosa	Colon
41	chr3:178788400-178790400	Active TSS	Colon Smooth Muscle	Colon
42	chr3:178788400-178790400	Active TSS	Right Atrium	heart
43	chr3:178788600-178789800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:178788600-178790000	Bivalent/Poised TSS	HepG2	liver
45	chr3:178788600-178790200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr3:178788600-178790200	Active TSS	Right Ventricle	heart
47	chr3:178788600-178790400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:178788600-178790400	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:178788800-178789600	Active TSS	Fetal Brain Male	brain
50	chr3:178788800-178789800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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