Variant report

Variant	rs563087744
Chromosome Location	chr3:52001411-52001412
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:96)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:96 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HMGN3	chr3:52001252-52002142	K562	blood:	n/a	n/a
2	PBX3	chr3:52001160-52002567	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:52001287-52002060	U87	brain:	n/a	n/a
4	POLR2A	chr3:52001331-52001485	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:52001150-52002505	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:52001030-52002404	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr3:52001182-52001610	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52001204-52002449	ProgFib	skin:	n/a	n/a
9	POLR2A	chr3:52001159-52002450	MCF-7	breast:	n/a	n/a
10	SIN3AK20	chr3:52001334-52001512	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:52001321-52002122	GM18505	blood:	n/a	n/a
12	MYC	chr3:52001383-52001462	MCF-7	breast:	n/a	n/a
13	E2F6	chr3:52001103-52001454	K562	blood:	n/a	n/a
14	SMARCB1	chr3:52000924-52002227	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:52001273-52002172	IMR90	lung:	n/a	n/a
16	ZBTB7A	chr3:52000806-52002473	ECC-1	luminal epithelium:	n/a	chr3:52002005-52002016
17	POLR2A	chr3:52001269-52003231	K562	blood:	n/a	n/a
18	TAF1	chr3:52001258-52002112	HepG2	liver:	n/a	n/a
19	YY1	chr3:52001248-52002430	HepG2	liver:	n/a	n/a
20	JUND	chr3:52001117-52001571	A549	lung:	n/a	n/a
21	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:52001349-52001493	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:52001269-52002160	GM15510	blood:	n/a	n/a
24	MAX	chr3:52000959-52003042	HepG2	liver:	n/a	chr3:52002253-52002263
25	POLR2A	chr3:52001329-52001482	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAZ	chr3:52001116-52002346	Hela-S3	cervix:	n/a	chr3:52002253-52002263
27	POLR2A	chr3:52001408-52002328	NB4	blood:	n/a	n/a
28	POLR2A	chr3:52001322-52002351	HEK293	kidney:	n/a	n/a
29	POLR2A	chr3:52000993-52002724	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr3:52001037-52001502	K562	blood:	n/a	n/a
31	POLR2A	chr3:52000905-52002797	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr3:52001330-52002720	SK-N-SH	brain:	n/a	n/a
33	JUND	chr3:52001394-52001510	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAZ	chr3:52001148-52001809	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:52001100-52002469	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:52001184-52002480	MCF-7	breast:	n/a	n/a
37	POLR2A	chr3:52001054-52001419	HepG2	liver:	n/a	n/a
38	PBX3	chr3:52001253-52002116	SK-N-SH	brain:	n/a	n/a
39	MXI1	chr3:52000907-52002412	IMR90	lung:	n/a	n/a
40	POLR2A	chr3:52001050-52002378	HCT-116	colon:	n/a	n/a
41	POLR2A	chr3:52001256-52001506	HCT-116	colon:	n/a	n/a
42	TAF1	chr3:52001271-52001506	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3A	chr3:52001041-52002724	H1-hESC	embryonic stem cell:	n/a	chr3:52001042-52001056 chr3:52002033-52002046
44	UBTF	chr3:52001292-52002174	K562	blood:	n/a	n/a
45	MAX	chr3:52001279-52001501	K562	blood:	n/a	n/a
46	JUND	chr3:52001320-52001500	K562	blood:	n/a	n/a
47	POLR2A	chr3:52001169-52003046	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:52001271-52002116	GM18951	blood:	n/a	n/a
49	CCNT2	chr3:52001242-52002310	K562	blood:	n/a	chr3:52001718-52001727
50	SMC3	chr3:52000928-52001453	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
2	chr3:51996322..51998656-chr3:51999527..52001457,4	MCF-7	breast:
3	chr3:51987928..51991924-chr3:52001407..52003695,4	MCF-7	breast:
4	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
5	chr3:51997248..52000056-chr3:52000079..52001783,2	MCF-7	breast:
6	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
7	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:

No data

Variant related genes	Relation type
PCBP4	TF binding region
ABHD14A	TF binding region
ENSG00000090097	Chromatin interaction
ENSG00000180929	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000041880	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52000200-52002000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:52000200-52002200	Active TSS	HSMMtube	muscle
3	chr3:52000400-52002000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr3:52000400-52002600	Active TSS	Fetal Kidney	kidney
5	chr3:52000400-52002600	Active TSS	Rectal Smooth Muscle	rectum
6	chr3:52000600-52002200	Active TSS	Brain Substantia Nigra	brain
7	chr3:52000600-52002200	Active TSS	Gastric	stomach
8	chr3:52000600-52002400	Active TSS	NHDF-Ad	bronchial
9	chr3:52000600-52002600	Active TSS	Brain Anterior Caudate	brain
10	chr3:52000800-52001600	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:52000800-52002000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:52000800-52002000	Active TSS	Brain Hippocampus Middle	brain
13	chr3:52000800-52002200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:52000800-52002200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:52000800-52002200	Active TSS	Brain Cingulate Gyrus	brain
16	chr3:52000800-52002200	Active TSS	Right Atrium	heart
17	chr3:52000800-52002400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:52000800-52002400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:52000800-52002400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:52000800-52002400	Active TSS	NHLF	lung
21	chr3:52000800-52002600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:52000800-52002600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:52000800-52002600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:52000800-52002600	Active TSS	A549	lung
25	chr3:52001000-52002000	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr3:52001000-52002000	Active TSS	Small Intestine	intestine
27	chr3:52001000-52002200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:52001000-52002200	Active TSS	Left Ventricle	heart
29	chr3:52001000-52002200	Active TSS	Lung	lung
30	chr3:52001000-52002400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:52001000-52002600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:52001000-52002600	Active TSS	Aorta	Aorta
33	chr3:52001200-52001600	Active TSS	Primary B cells from cord blood	blood
34	chr3:52001200-52001600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:52001200-52001800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr3:52001200-52001800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:52001200-52002000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:52001200-52002000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:52001200-52002000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:52001200-52002000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:52001200-52002000	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
42	chr3:52001200-52002000	Active TSS	Primary B cells from peripheral blood	blood
43	chr3:52001200-52002000	Active TSS	Primary T cells fromperipheralblood	blood
44	chr3:52001200-52002000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:52001200-52002000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr3:52001200-52002000	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:52001200-52002000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:52001200-52002000	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr3:52001200-52002000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr3:52001200-52002000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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