Variant report

Variant	rs555216056
Chromosome Location	chr3:52568026-52568027
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:288)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:288 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52567960-52568110	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr3:52567980-52568130	NHLF	lung:	n/a	n/a
3	POLR2A	chr3:52567956-52568200	HCT-116	colon:	n/a	n/a
4	MAX	chr3:52567694-52568280	A549	lung:	n/a	n/a
5	POLR2A	chr3:52567801-52568278	HUVEC	blood vessel:	n/a	n/a
6	TAF1	chr3:52567823-52568240	ECC-1	luminal epithelium:	n/a	n/a
7	ELF1	chr3:52567793-52568333	GM12878	blood:	n/a	chr3:52567885-52567897
8	CTCF	chr3:52567999-52568091	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:52567952-52568196	SK-N-MC	brain:	n/a	n/a
10	RFX5	chr3:52568020-52568034	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:52567916-52568156	A549	lung:	n/a	n/a
12	SIN3AK20	chr3:52567910-52568157	HepG2	liver:	n/a	n/a
13	MAX	chr3:52567694-52568169	SK-N-SH	brain:	n/a	n/a
14	ZBTB7A	chr3:52567836-52568169	HepG2	liver:	n/a	n/a
15	CHD2	chr3:52567981-52568162	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr3:52567391-52568185	ECC-1	luminal epithelium:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
17	CTCF	chr3:52567920-52568070	HCM	heart:	n/a	n/a
18	POLR2A	chr3:52567986-52568077	MCF-7	breast:	n/a	n/a
19	MYC	chr3:52567987-52568033	HUVEC	blood vessel:	n/a	n/a
20	NFYB	chr3:52567559-52568304	GM12878	blood:	n/a	chr3:52567864-52567879 chr3:52567861-52567876 chr3:52567864-52567879 chr3:52567864-52567878
21	CTCF	chr3:52567980-52568130	SK-N-SH_RA	brain:	n/a	n/a
22	MAX	chr3:52567970-52568127	GM12878	blood:	n/a	n/a
23	YY1	chr3:52567786-52568597	HepG2	liver:	n/a	chr3:52567878-52567892 chr3:52567972-52567983
24	POLR2A	chr3:52566536-52568278	GM15510	blood:	n/a	n/a
25	CTCF	chr3:52567960-52568110	NHDF-neo	bronchial:	n/a	n/a
26	POLR2A	chr3:52567449-52568224	HEK293	kidney:	n/a	n/a
27	MYC	chr3:52567965-52568128	MCF10A-Er-Src	breast:	n/a	n/a
28	CHD2	chr3:52567513-52568198	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:52567940-52568130	A549	lung:	n/a	n/a
30	CTCF	chr3:52567980-52568130	AG09319	gingival:	n/a	n/a
31	CTCF	chr3:52567940-52568090	AG04450	lung:	n/a	n/a
32	TAF1	chr3:52567922-52568163	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:52567801-52568351	HUVEC	blood vessel:	n/a	n/a
34	JUND	chr3:52567968-52568139	H1-hESC	embryonic stem cell:	n/a	n/a
35	UBTF	chr3:52567975-52568263	K562	blood:	n/a	n/a
36	ZBTB7A	chr3:52567830-52568199	K562	blood:	n/a	chr3:52568173-52568181
37	FOS	chr3:52567721-52568050	K562	blood:	n/a	n/a
38	POLR2A	chr3:52567933-52568208	HepG2	liver:	n/a	n/a
39	RCOR1	chr3:52567965-52568132	GM12878	blood:	n/a	n/a
40	CTCF	chr3:52567960-52568110	GM12871	blood:	n/a	n/a
41	POLR2A	chr3:52567427-52568232	GM18505	blood:	n/a	n/a
42	RXRA	chr3:52567802-52568114	GM12878	blood:	n/a	n/a
43	MAX	chr3:52567337-52569379	HepG2	liver:	n/a	n/a
44	MXI1	chr3:52566450-52569219	IMR90	lung:	n/a	n/a
45	CTCF	chr3:52567960-52568110	BJ	skin:	n/a	n/a
46	CTCF	chr3:52567960-52568110	GM12875	blood:	n/a	n/a
47	POLR2A	chr3:52566494-52568343	GM12892	blood:	n/a	n/a
48	CTCF	chr3:52567960-52568110	GM12864	blood:	n/a	n/a
49	CEBPD	chr3:52567923-52568175	HepG2	liver:	n/a	n/a
50	MAX	chr3:52567368-52568098	NB4	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52567779..52572340-chr3:52718708..52722750,6	K562	blood:
2	chr22:47133970..47134516-chr3:52567792..52568293,2	HCT-116	colon:
3	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:
4	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
5	chr3:52567230..52568070-chr9:131218351..131218852,2	Hela-S3	cervix:
6	chr3:52567315..52569798-chr3:52739141..52741499,3	MCF-7	breast:
7	chr3:52566165..52568026-chr3:52648479..52651083,2	K562	blood:
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	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
12	chr3:52567128..52569011-chr3:52738941..52741649,3	K562	blood:
13	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
14	chr3:52444067..52446922-chr3:52566590..52568238,2	K562	blood:
15	chr3:52566406..52569677-chr3:52718507..52721358,5	MCF-7	breast:
16	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
17	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:

No data

Variant related genes	Relation type
NT5DC2	TF binding region
SMIM4	TF binding region
ENSG00000010327	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000100422	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000136811	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000163938	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	esv11293	chr3:52567550-52568100	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	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	chr3:52566200-52569000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:52566200-52571600	Active TSS	Fetal Kidney	kidney
3	chr3:52566400-52568600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52566400-52568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:52566400-52569000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:52566600-52568400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:52566600-52568400	Active TSS	Brain Angular Gyrus	brain
8	chr3:52566600-52568600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:52566600-52568600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:52566600-52568600	Active TSS	A549	lung
11	chr3:52566600-52568800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:52566800-52568200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr3:52566800-52568200	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr3:52566800-52568400	Active TSS	NH-A	brain
15	chr3:52566800-52568600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:52566800-52568600	Active TSS	HSMMtube	muscle
17	chr3:52566800-52568800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr3:52566800-52568800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr3:52566800-52568800	Active TSS	Rectal Smooth Muscle	rectum
20	chr3:52566800-52569000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:52566800-52569200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:52566800-52569200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:52566800-52569400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr3:52567000-52568200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:52567000-52568200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:52567000-52568200	Active TSS	Primary T cells from cord blood	blood
27	chr3:52567000-52568200	Active TSS	Muscle Satellite Cultured Cells	--
28	chr3:52567000-52568200	Active TSS	Brain Anterior Caudate	brain
29	chr3:52567000-52568200	Active TSS	Duodenum Mucosa	Duodenum
30	chr3:52567000-52568200	Active TSS	Esophagus	oesophagus
31	chr3:52567000-52568200	Active TSS	Fetal Stomach	stomach
32	chr3:52567000-52568200	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr3:52567000-52568200	Active TSS	Small Intestine	intestine
34	chr3:52567000-52568200	Active TSS	GM12878-XiMat	blood
35	chr3:52567000-52568200	Active TSS	Hela-S3	cervix
36	chr3:52567000-52568200	Active TSS	HepG2	liver
37	chr3:52567000-52568200	Active TSS	HUVEC	blood vessel
38	chr3:52567000-52568200	Active TSS	Osteobl	bone
39	chr3:52567000-52568400	Active TSS	H1 Cell Line	embryonic stem cell
40	chr3:52567000-52568400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:52567000-52568400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52567000-52568400	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:52567000-52568400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:52567000-52568400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:52567000-52568400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:52567000-52568400	Active TSS	Brain Cingulate Gyrus	brain
47	chr3:52567000-52568400	Weak transcription	Fetal Heart	heart
48	chr3:52567000-52568400	Active TSS	K562	blood
49	chr3:52567000-52568400	Active TSS	NHEK	skin
50	chr3:52567000-52568600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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