Variant report

Variant	rs531683534
Chromosome Location	chr3:52001967-52001968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:124)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:124 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52001600-52002334	GM12878	blood:	n/a	n/a
2	HMGN3	chr3:52001252-52002142	K562	blood:	n/a	n/a
3	GABPA	chr3:52001587-52002097	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:52001531-52002263	HUVEC	blood vessel:	n/a	n/a
5	MTA3	chr3:52001768-52002453	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:52001867-52002343	U87	brain:	n/a	n/a
7	TAF1	chr3:52001737-52002219	H1-neurons	neurons:	n/a	n/a
8	PBX3	chr3:52001160-52002567	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:52001287-52002060	U87	brain:	n/a	n/a
10	POLR2A	chr3:52001585-52002349	U87	brain:	n/a	n/a
11	POLR2A	chr3:52001150-52002505	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr3:52001846-52002673	H1-hESC	embryonic stem cell:	n/a	chr3:52002253-52002263
13	POLR2A	chr3:52001030-52002404	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:52001204-52002449	ProgFib	skin:	n/a	n/a
15	POLR2A	chr3:52001159-52002450	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:52001880-52002447	HepG2	liver:	n/a	n/a
17	ELF1	chr3:52001591-52002024	K562	blood:	n/a	chr3:52001964-52001976
18	POLR2A	chr3:52001835-52002126	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr3:52001900-52002096	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:52001321-52002122	GM18505	blood:	n/a	n/a
21	POLR2A	chr3:52001630-52002101	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:52001856-52002127	H1-hESC	embryonic stem cell:	n/a	n/a
23	SMARCB1	chr3:52000924-52002227	Hela-S3	cervix:	n/a	n/a
24	MAX	chr3:52001841-52002225	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:52001273-52002172	IMR90	lung:	n/a	n/a
26	POLR2A	chr3:52001550-52002185	ECC-1	luminal epithelium:	n/a	n/a
27	ZBTB7A	chr3:52000806-52002473	ECC-1	luminal epithelium:	n/a	chr3:52002005-52002016
28	POLR2A	chr3:52001269-52003231	K562	blood:	n/a	n/a
29	TAF1	chr3:52001258-52002112	HepG2	liver:	n/a	n/a
30	YY1	chr3:52001248-52002430	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:52001564-52002096	A549	lung:	n/a	n/a
32	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:52001269-52002160	GM15510	blood:	n/a	n/a
34	MAX	chr3:52000959-52003042	HepG2	liver:	n/a	chr3:52002253-52002263
35	POLR2A	chr3:52001850-52003171	HepG2	liver:	n/a	n/a
36	TAF1	chr3:52001959-52002179	SK-N-SH	brain:	n/a	n/a
37	MAZ	chr3:52001116-52002346	Hela-S3	cervix:	n/a	chr3:52002253-52002263
38	CTCF	chr3:52001900-52002050	GM12875	blood:	n/a	n/a
39	POLR2A	chr3:52001408-52002328	NB4	blood:	n/a	n/a
40	POLR2A	chr3:52001322-52002351	HEK293	kidney:	n/a	n/a
41	RCOR1	chr3:52001944-52002126	K562	blood:	n/a	n/a
42	POLR2A	chr3:52001956-52002131	Raji	blood:	n/a	n/a
43	POLR2A	chr3:52000993-52002724	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr3:52000905-52002797	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr3:52001330-52002720	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr3:52001100-52002469	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:52001573-52002273	GM12892	blood:	n/a	n/a
48	POLR2A	chr3:52001184-52002480	MCF-7	breast:	n/a	n/a
49	PBX3	chr3:52001253-52002116	SK-N-SH	brain:	n/a	n/a
50	MXI1	chr3:52000907-52002412	IMR90	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52001952-52002002	ProgFib	skin:	n/a
2	chr3:52001952-52002002	LNCaP	prostate:	n/a
3	chr3:52001952-52002002	AG09319	gingival:	n/a
4	chr3:52001952-52002002	U87	brain:	n/a
5	chr3:52001952-52002002	HepG2	liver:	n/a
6	chr3:52001952-52002002	HRCEpiC	kidney:	n/a
7	chr3:52001952-52002002	NB4	blood:	n/a
8	chr3:52001952-52002002	SK-N-SH_RA	brain:	n/a
9	chr3:52001952-52002002	HCM	heart:	n/a
10	chr3:52001952-52002002	AG09309	skin:	n/a
11	chr3:52001952-52002002	HMEC	breast:	n/a
12	chr3:52001952-52002002	H1-hESC	embryonic stem cell:	embryo
13	chr3:52001952-52002002	HEEpiC	esophagus:	n/a
14	chr3:52001952-52002002	SK-N-MC	brain:	n/a
15	chr3:52001952-52002002	SKMC	muscle:	n/a
16	chr3:52001952-52002002	NHBE	bronchial:	n/a
17	chr3:52001952-52002002	GM12891	blood:	n/a
18	chr3:52001952-52002002	RPTEC	kidney:	n/a
19	chr3:52001952-52002002	PrEC	prostate:	n/a
20	chr3:52001952-52002002	GM19239	blood:	n/a
21	chr3:52001952-52002002	HRPEpiC	eye:	n/a
22	chr3:52001952-52002002	HRE	kidney:	n/a
23	chr3:52001952-52002002	NHDF-neo	bronchial:	n/a
24	chr3:52001952-52002002	GM12892	blood:	n/a
25	chr3:52001952-52002002	GM06990	blood:	n/a
26	chr3:52001952-52002002	HPAEpiC	pulmonary alveolar:	n/a
27	chr3:52001952-52002002	PFSK-1	brain:	n/a
28	chr3:52001952-52002002	MCF10A-Er-Src	breast:	n/a
29	chr3:52001952-52002002	Jurkat	blood:	n/a
30	chr3:52001952-52002002	HIPEpiC	eye:	n/a
31	chr3:52001952-52002002	HCPEpiC	choroid plexus:	n/a
32	chr3:52001952-52002002	Caco-2	colon:	n/a
33	chr3:52001952-52002002	ECC-1	luminal epithelium:	n/a
34	chr3:52001952-52002002	NH-A	brain:	n/a
35	chr3:52001952-52002002	A549	lung:	n/a
36	chr3:52001952-52002002	AoSMC	blood vessel:	n/a
37	chr3:52001952-52002002	K562	blood:	n/a
38	chr3:52001952-52002002	Hepatocyte	liver:	n/a
39	chr3:52001952-52002002	AG04450	lung:	fetal
40	chr3:52001952-52002002	HCT-116	colon:	n/a
41	chr3:52001952-52002002	PANC-1	pancreas:	n/a
42	chr3:52001952-52002002	HEK293	kidney:	embryo
43	chr3:52001952-52002002	NT2-D1	testis:	n/a
44	chr3:52001952-52002002	HCF	heart:	n/a
45	chr3:52001952-52002002	GM12878	blood:	n/a
46	chr3:52001952-52002002	ovcar-3	ovarian:	n/a
47	chr3:52001952-52002002	Hela-S3	cervix:	n/a
48	chr3:52001952-52002002	HUVEC	blood vessel:	n/a
49	chr3:52001952-52002002	AG04449	skin:	fetal
50	chr3:52001952-52002002	BJ	skin:	n/a

(count:8 , 50 per page) page: 1

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	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
8	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
ABHD14A	CpG island
PCBP4	CpG island
ENSG00000180929	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000145050	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000114767	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	chr3:52000800-52002000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:52000800-52002000	Active TSS	Brain Hippocampus Middle	brain
12	chr3:52000800-52002200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:52000800-52002200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:52000800-52002200	Active TSS	Brain Cingulate Gyrus	brain
15	chr3:52000800-52002200	Active TSS	Right Atrium	heart
16	chr3:52000800-52002400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:52000800-52002400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:52000800-52002400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:52000800-52002400	Active TSS	NHLF	lung
20	chr3:52000800-52002600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:52000800-52002600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:52000800-52002600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:52000800-52002600	Active TSS	A549	lung
24	chr3:52001000-52002000	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr3:52001000-52002000	Active TSS	Small Intestine	intestine
26	chr3:52001000-52002200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:52001000-52002200	Active TSS	Left Ventricle	heart
28	chr3:52001000-52002200	Active TSS	Lung	lung
29	chr3:52001000-52002400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:52001000-52002600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr3:52001000-52002600	Active TSS	Aorta	Aorta
32	chr3:52001200-52002000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:52001200-52002000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:52001200-52002000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:52001200-52002000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:52001200-52002000	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
37	chr3:52001200-52002000	Active TSS	Primary B cells from peripheral blood	blood
38	chr3:52001200-52002000	Active TSS	Primary T cells fromperipheralblood	blood
39	chr3:52001200-52002000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:52001200-52002000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr3:52001200-52002000	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr3:52001200-52002000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:52001200-52002000	Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr3:52001200-52002000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr3:52001200-52002000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:52001200-52002000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:52001200-52002000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr3:52001200-52002000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:52001200-52002000	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:52001200-52002000	Active TSS	Cortex derived primary cultured neurospheres	brain

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