Variant report

Variant	rs556119574
Chromosome Location	chr3:52567461-52567462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:95)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:95 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:52567337-52567564	GM12878	blood:	n/a	n/a
2	YY1	chr3:52567391-52568185	ECC-1	luminal epithelium:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
3	POLR2A	chr3:52566966-52567850	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:52566536-52568278	GM15510	blood:	n/a	n/a
5	POLR2A	chr3:52567449-52568224	HEK293	kidney:	n/a	n/a
6	POLR2A	chr3:52565978-52567545	U87	brain:	n/a	n/a
7	POLR2A	chr3:52567427-52568232	GM18505	blood:	n/a	n/a
8	MAX	chr3:52567337-52569379	HepG2	liver:	n/a	n/a
9	MXI1	chr3:52566450-52569219	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:52566494-52568343	GM12892	blood:	n/a	n/a
11	MAX	chr3:52567368-52568098	NB4	blood:	n/a	n/a
12	PBX3	chr3:52567389-52567532	GM12878	blood:	n/a	n/a
13	CCNT2	chr3:52566580-52568816	K562	blood:	n/a	chr3:52566977-52566986 chr3:52567974-52567983 chr3:52567185-52567194 chr3:52567981-52567990
14	UBTF	chr3:52566770-52567678	K562	blood:	n/a	n/a
15	POLR2A	chr3:52565799-52567472	HepG2	liver:	n/a	n/a
16	MYC	chr3:52567416-52567474	K562	blood:	n/a	n/a
17	HMGN3	chr3:52566706-52568905	K562	blood:	n/a	n/a
18	MAZ	chr3:52567452-52568161	Hela-S3	cervix:	n/a	n/a
19	HA-E2F1	chr3:52567385-52568072	Hela-S3	cervix:	n/a	n/a
20	MAX	chr3:52567064-52568083	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:52567417-52568187	Gliobla	brain:	n/a	n/a
22	E2F6	chr3:52567290-52569157	K562	blood:	n/a	n/a
23	POLR2A	chr3:52566562-52568130	GM12878	blood:	n/a	n/a
24	TCF3	chr3:52567376-52567819	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:52567422-52568418	MCF-7	breast:	n/a	n/a
26	TAF1	chr3:52567378-52568288	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:52565761-52567641	U87	brain:	n/a	n/a
28	UBTF	chr3:52566448-52567664	K562	blood:	n/a	n/a
29	MAX	chr3:52567242-52567631	A549	lung:	n/a	n/a
30	POLR2A	chr3:52567367-52567909	Hela-S3	cervix:	n/a	n/a
31	ZBTB7A	chr3:52567016-52568425	ECC-1	luminal epithelium:	n/a	chr3:52568173-52568181
32	MAX	chr3:52567066-52568226	H1-hESC	embryonic stem cell:	n/a	n/a
33	HEY1	chr3:52567360-52567583	K562	blood:	n/a	n/a
34	POLR2A	chr3:52566714-52569188	MCF-7	breast:	n/a	n/a
35	MAX	chr3:52567313-52569354	HepG2	liver:	n/a	n/a
36	MAX	chr3:52567187-52568696	A549	lung:	n/a	n/a
37	POLR2A	chr3:52567370-52567929	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr3:52567446-52568195	Raji	blood:	n/a	n/a
39	MXI1	chr3:52567072-52567524	Hela-S3	cervix:	n/a	n/a
40	E2F6	chr3:52567435-52567710	K562	blood:	n/a	n/a
41	CHD2	chr3:52567348-52568163	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:52567330-52567917	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr3:52567407-52567906	HUVEC	blood vessel:	n/a	n/a
44	ZBTB7A	chr3:52567147-52567720	K562	blood:	n/a	n/a
45	POLR2A	chr3:52566584-52568241	GM18951	blood:	n/a	n/a
46	POLR2A	chr3:52566150-52567589	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr3:52567457-52567912	A549	lung:	n/a	n/a
48	POLR2A	chr3:52567435-52567913	A549	lung:	n/a	n/a
49	MAZ	chr3:52566465-52567568	GM12878	blood:	n/a	chr3:52566595-52566603
50	MAX	chr3:52567420-52567621	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:
2	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
3	chr3:52567230..52568070-chr9:131218351..131218852,2	Hela-S3	cervix:
4	chr3:52567015..52567802-chr3:186500888..186501659,2	Hela-S3	cervix:
5	chr3:52567315..52569798-chr3:52739141..52741499,3	MCF-7	breast:
6	chr3:52566165..52568026-chr3:52648479..52651083,2	K562	blood:
7	chr15:65596638..65597519-chr3:52567379..52568024,2	HCT-116	colon:
8	chr3:52504515..52506973-chr3:52565446..52568302,2	MCF-7	breast:
9	chr3:52551484..52554158-chr3:52567066..52569157,2	MCF-7	breast:
10	chr3:52503525..52506168-chr3:52566167..52568849,2	MCF-7	breast:
11	chr3:52567128..52569011-chr3:52738941..52741649,3	K562	blood:
12	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
13	chr3:52444067..52446922-chr3:52566590..52568238,2	K562	blood:
14	chr3:52566406..52569677-chr3:52718507..52721358,5	MCF-7	breast:
15	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
16	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:

No data

Variant related genes	Relation type
SMIM4	TF binding region
NT5DC2	TF binding region
ENSG00000016864	Chromatin interaction
ENSG00000156976	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000136811	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	esv3389739	chr3:52566962-52569135	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr3:52566200-52567600	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr3:52566200-52569000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:52566200-52571600	Active TSS	Fetal Kidney	kidney
4	chr3:52566400-52568600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:52566400-52568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:52566400-52569000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:52566600-52567600	Flanking Active TSS	Colonic Mucosa	Colon
8	chr3:52566600-52567600	Flanking Active TSS	Placenta	Placenta
9	chr3:52566600-52567600	Flanking Active TSS	Right Ventricle	heart
10	chr3:52566600-52567800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr3:52566600-52567800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52566600-52568400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:52566600-52568400	Active TSS	Brain Angular Gyrus	brain
14	chr3:52566600-52568600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:52566600-52568600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:52566600-52568600	Active TSS	A549	lung
17	chr3:52566600-52568800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr3:52566800-52567600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
19	chr3:52566800-52567600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:52566800-52568200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:52566800-52568200	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr3:52566800-52568400	Active TSS	NH-A	brain
23	chr3:52566800-52568600	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:52566800-52568600	Active TSS	HSMMtube	muscle
25	chr3:52566800-52568800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:52566800-52568800	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:52566800-52568800	Active TSS	Rectal Smooth Muscle	rectum
28	chr3:52566800-52569000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:52566800-52569200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:52566800-52569200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:52566800-52569400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr3:52567000-52567600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr3:52567000-52567600	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr3:52567000-52567600	Enhancers	Fetal Brain Male	brain
35	chr3:52567000-52567600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:52567000-52567800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:52567000-52568000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr3:52567000-52568200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:52567000-52568200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:52567000-52568200	Active TSS	Primary T cells from cord blood	blood
41	chr3:52567000-52568200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:52567000-52568200	Active TSS	Brain Anterior Caudate	brain
43	chr3:52567000-52568200	Active TSS	Duodenum Mucosa	Duodenum
44	chr3:52567000-52568200	Active TSS	Esophagus	oesophagus
45	chr3:52567000-52568200	Active TSS	Fetal Stomach	stomach
46	chr3:52567000-52568200	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr3:52567000-52568200	Active TSS	Small Intestine	intestine
48	chr3:52567000-52568200	Active TSS	GM12878-XiMat	blood
49	chr3:52567000-52568200	Active TSS	Hela-S3	cervix
50	chr3:52567000-52568200	Active TSS	HepG2	liver

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