Variant report

Variant	rs545533998
Chromosome Location	chr3:52002581-52002582
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	CHD2	chr3:52002430-52002639	K562	blood:	n/a	n/a
2	MAX	chr3:52001846-52002673	H1-hESC	embryonic stem cell:	n/a	chr3:52002253-52002263
3	POLR2A	chr3:52002454-52002990	HepG2	liver:	n/a	n/a
4	HNF4G	chr3:52002266-52002614	HepG2	liver:	n/a	chr3:52002418-52002430 chr3:52002415-52002430 chr3:52002421-52002429 chr3:52002417-52002431
5	POLR2A	chr3:52001269-52003231	K562	blood:	n/a	n/a
6	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
7	MAX	chr3:52000959-52003042	HepG2	liver:	n/a	chr3:52002253-52002263
8	POLR2A	chr3:52001850-52003171	HepG2	liver:	n/a	n/a
9	MYC	chr3:52002271-52002683	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr3:52002217-52002604	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:52000993-52002724	H1-neurons	neurons:	n/a	n/a
12	JUND	chr3:52002241-52002675	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:52000905-52002797	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr3:52001330-52002720	SK-N-SH	brain:	n/a	n/a
15	CEBPB	chr3:52002396-52002720	H1-hESC	embryonic stem cell:	n/a	chr3:52002533-52002544
16	CEBPB	chr3:52002418-52002602	HepG2	liver:	n/a	chr3:52002533-52002544
17	CHD2	chr3:52002123-52002659	H1-hESC	embryonic stem cell:	n/a	chr3:52002329-52002339
18	SIN3A	chr3:52001041-52002724	H1-hESC	embryonic stem cell:	n/a	chr3:52001042-52001056 chr3:52002033-52002046
19	MAX	chr3:52001743-52002645	H1-hESC	embryonic stem cell:	n/a	chr3:52002253-52002263
20	POLR2A	chr3:52001169-52003046	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr3:52002122-52002595	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAZ	chr3:52000663-52002637	IMR90	lung:	n/a	chr3:52002253-52002263
23	POLR2A	chr3:52001612-52003896	K562	blood:	n/a	n/a
24	TBP	chr3:52002047-52002616	H1-hESC	embryonic stem cell:	n/a	n/a
25	REST	chr3:52000680-52002949	H1-neurons	neurons:	n/a	chr3:52000755-52000768 chr3:52002487-52002500 chr3:52001970-52001983 chr3:52001041-52001061 chr3:52001961-52001979 chr3:52002033-52002046 chr3:52002331-52002344 chr3:52001963-52001976 chr3:52001141-52001154 chr3:52002454-52002467
26	POLR2A	chr3:52002472-52003126	PFSK-1	brain:	n/a	n/a
27	TEAD4	chr3:52001930-52002594	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:52002485-52002819	K562	blood:	n/a	n/a
29	ZBTB7A	chr3:52000994-52002818	ECC-1	luminal epithelium:	n/a	chr3:52002005-52002016
30	CEBPB	chr3:52002382-52002704	HepG2	liver:	n/a	chr3:52002533-52002544
31	EP300	chr3:52002173-52002583	SK-N-SH_RA	brain:	n/a	n/a
32	POLR2A	chr3:52001398-52003148	Hela-S3	cervix:	n/a	n/a
33	CTBP2	chr3:52001997-52002726	H1-hESC	embryonic stem cell:	n/a	n/a
34	CEBPB	chr3:52002525-52002704	K562	blood:	n/a	chr3:52002533-52002544
35	ELF1	chr3:52000829-52002584	GM12878	blood:	n/a	chr3:52001964-52001976 chr3:52001478-52001490
36	POLR2A	chr3:52002457-52002702	K562	blood:	n/a	n/a
37	MYC	chr3:52001690-52003070	NB4	blood:	n/a	chr3:52002253-52002263
38	MXI1	chr3:51999719-52003632	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr3:52002159-52002695	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:52001525-52003872	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:52000980-52003171	Hela-S3	cervix:	n/a	n/a
42	EP300	chr3:52002159-52002595	HepG2	liver:	n/a	n/a
43	POLR2A	chr3:52001602-52003298	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr3:52001593-52002642	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:52001867-52002725	H1-hESC	embryonic stem cell:	n/a	n/a
46	CEBPB	chr3:52002494-52002714	Hela-S3	cervix:	n/a	chr3:52002533-52002544
47	POLR2A	chr3:52001537-52003111	HCT-116	colon:	n/a	n/a
48	SP1	chr3:52002239-52002711	H1-hESC	embryonic stem cell:	n/a	chr3:52002458-52002467 chr3:52002491-52002500 chr3:52002453-52002467 chr3:52002456-52002468 chr3:52002325-52002339 chr3:52002457-52002466 chr3:52002489-52002501 chr3:52002456-52002468 chr3:52002489-52002501 chr3:52002457-52002467 chr3:52002252-52002264 chr3:52002490-52002500 chr3:52002254-52002263 chr3:52002490-52002499 chr3:52002486-52002500 chr3:52002252-52002264
49	CHD2	chr3:52000996-52002698	Hela-S3	cervix:	n/a	chr3:52002329-52002339

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52002555-52002605	NHDF-neo	bronchial:	n/a
2	chr3:52002555-52002605	ovcar-3	ovarian:	n/a
3	chr3:52002555-52002605	ECC-1	luminal epithelium:	n/a
4	chr3:52002555-52002605	HEK293	kidney:	embryo
5	chr3:52002555-52002605	AG04449	skin:	fetal
6	chr3:52002555-52002605	NT2-D1	testis:	n/a
7	chr3:52002555-52002605	HRCEpiC	kidney:	n/a
8	chr3:52002555-52002605	GM19239	blood:	n/a
9	chr3:52002555-52002605	IMR90	lung:	fetal
10	chr3:52002555-52002605	NHBE	bronchial:	n/a
11	chr3:52002555-52002605	HAEpiC	amniotic membrane:	n/a
12	chr3:52002555-52002605	Hela-S3	cervix:	n/a
13	chr3:52002555-52002605	ProgFib	skin:	n/a
14	chr3:52002555-52002605	LNCaP	prostate:	n/a
15	chr3:52002555-52002605	GM12891	blood:	n/a
16	chr3:52002555-52002605	Hepatocyte	liver:	n/a
17	chr3:52002555-52002605	BE2_C	brain:	n/a
18	chr3:52002555-52002605	SAEC	small airway:	n/a
19	chr3:52002555-52002605	Caco-2	colon:	n/a
20	chr3:52002555-52002605	GM06990	blood:	n/a
21	chr3:52002555-52002605	AG09319	gingival:	n/a
22	chr3:52002555-52002605	NH-A	brain:	n/a
23	chr3:52002555-52002605	CMK	blood:	n/a
24	chr3:52002555-52002605	HL-60	blood:	n/a
25	chr3:52002555-52002605	SKMC	muscle:	n/a
26	chr3:52002555-52002605	K562	blood:	n/a
27	chr3:52002555-52002605	HNPCEpiC	eye:	n/a
28	chr3:52002555-52002605	U87	brain:	n/a
29	chr3:52002555-52002605	HCM	heart:	n/a
30	chr3:52002555-52002605	HUVEC	blood vessel:	n/a
31	chr3:52002555-52002605	HPAEpiC	pulmonary alveolar:	n/a
32	chr3:52002555-52002605	AG09309	skin:	n/a
33	chr3:52002555-52002605	RPTEC	kidney:	n/a
34	chr3:52002555-52002605	NB4	blood:	n/a
35	chr3:52002555-52002605	AG10803	skin:	n/a
36	chr3:52002555-52002605	GM12892	blood:	n/a
37	chr3:52002555-52002605	PANC-1	pancreas:	n/a
38	chr3:52002555-52002605	MCF10A-Er-Src	breast:	n/a
39	chr3:52002555-52002605	Jurkat	blood:	n/a
40	chr3:52002555-52002605	A549	lung:	n/a
41	chr3:52002555-52002605	SK-N-SH	brain:	n/a
42	chr3:52002555-52002605	HCF	heart:	n/a
43	chr3:52002555-52002605	HCPEpiC	choroid plexus:	n/a
44	chr3:52002555-52002605	AG04450	lung:	fetal
45	chr3:52002555-52002605	PFSK-1	brain:	n/a
46	chr3:52002555-52002605	PrEC	prostate:	n/a
47	chr3:52002555-52002605	MCF-7	breast:	n/a
48	chr3:52002555-52002605	HRE	kidney:	n/a
49	chr3:52002555-52002605	HCT-116	colon:	n/a
50	chr3:52002555-52002605	GM12878	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
2	chr3:51987928..51991924-chr3:52001407..52003695,4	MCF-7	breast:
3	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
4	chr3:51421943..51424034-chr3:52001693..52003789,2	MCF-7	breast:
5	chr3:51978894..51981977-chr3:52001614..52003382,3	MCF-7	breast:
6	chr3:52001556..52005448-chr3:52028528..52032420,5	MCF-7	breast:
7	chr3:51976428..51980212-chr3:52001978..52006587,6	MCF-7	breast:
8	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:

Variant related genes	Relation type
ABHD14A	TF binding region
PCBP4	TF binding region
ABHD14A	CpG island
PCBP4	CpG island
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000180929	Chromatin interaction
ENSG00000145050	Chromatin interaction
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	esv3403794	chr3:52000337-52003085	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52000400-52002600	Active TSS	Fetal Kidney	kidney
2	chr3:52000400-52002600	Active TSS	Rectal Smooth Muscle	rectum
3	chr3:52000600-52002600	Active TSS	Brain Anterior Caudate	brain
4	chr3:52000800-52002600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:52000800-52002600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:52000800-52002600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:52000800-52002600	Active TSS	A549	lung
8	chr3:52001000-52002600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:52001000-52002600	Active TSS	Aorta	Aorta
10	chr3:52001200-52002600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:52001200-52002600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:52001200-52002600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:52001200-52002600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:52001200-52002600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:52001200-52002600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:52001800-52002600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:52001800-52002800	Flanking Active TSS	Dnd41	blood
18	chr3:52001800-52003200	Enhancers	Fetal Heart	heart
19	chr3:52001800-52007600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:52002000-52002600	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr3:52002000-52002600	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr3:52002000-52002600	Flanking Active TSS	Thymus	Thymus
23	chr3:52002000-52002800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:52002000-52002800	Flanking Active TSS	Colonic Mucosa	Colon
25	chr3:52002000-52002800	Flanking Active TSS	HepG2	liver
26	chr3:52002000-52003000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:52002000-52003000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:52002000-52005800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:52002200-52002600	Enhancers	Primary B cells from cord blood	blood
30	chr3:52002200-52002800	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:52002200-52002800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:52002200-52002800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:52002200-52003000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:52002200-52003000	Flanking Active TSS	Fetal Brain Female	brain
35	chr3:52002200-52003000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr3:52002200-52003000	Enhancers	Small Intestine	intestine
37	chr3:52002200-52003200	Weak transcription	Gastric	stomach
38	chr3:52002200-52003400	Enhancers	Primary T cells from cord blood	blood
39	chr3:52002200-52003600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr3:52002200-52003600	Enhancers	Spleen	Spleen
41	chr3:52002200-52007400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:52002400-52002600	Active TSS	H1 Cell Line	embryonic stem cell
43	chr3:52002400-52002600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:52002400-52002600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr3:52002400-52002600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:52002400-52002600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:52002400-52002600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:52002400-52002600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:52002400-52002600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:52002400-52002600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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