Variant report

Variant	rs553413681
Chromosome Location	chr3:52002258-52002259
allele	G/T
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	POLR2A	chr3:52001600-52002334	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52001531-52002263	HUVEC	blood vessel:	n/a	n/a
3	MTA3	chr3:52001768-52002453	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:52001867-52002343	U87	brain:	n/a	n/a
5	PBX3	chr3:52001160-52002567	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:52001585-52002349	U87	brain:	n/a	n/a
7	TEAD4	chr3:52002174-52002489	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF2	chr3:52002182-52002380	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:52001150-52002505	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr3:52001846-52002673	H1-hESC	embryonic stem cell:	n/a	chr3:52002253-52002263
11	POLR2A	chr3:52001030-52002404	Hela-S3	cervix:	n/a	n/a
12	EGR1	chr3:52002240-52002458	K562	blood:	n/a	chr3:52002281-52002291 chr3:52002366-52002380 chr3:52002366-52002377
13	POLR2A	chr3:52001204-52002449	ProgFib	skin:	n/a	n/a
14	POLR2A	chr3:52001159-52002450	MCF-7	breast:	n/a	n/a
15	POLR2A	chr3:52001880-52002447	HepG2	liver:	n/a	n/a
16	RUNX3	chr3:52002248-52002503	GM12878	blood:	n/a	n/a
17	ZBTB7A	chr3:52002228-52002545	HepG2	liver:	n/a	n/a
18	ZBTB7A	chr3:52000806-52002473	ECC-1	luminal epithelium:	n/a	chr3:52002005-52002016
19	POLR2A	chr3:52001269-52003231	K562	blood:	n/a	n/a
20	YY1	chr3:52001248-52002430	HepG2	liver:	n/a	n/a
21	TCF12	chr3:52002225-52002476	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
23	MAX	chr3:52000959-52003042	HepG2	liver:	n/a	chr3:52002253-52002263
24	POLR2A	chr3:52001850-52003171	HepG2	liver:	n/a	n/a
25	MAZ	chr3:52001116-52002346	Hela-S3	cervix:	n/a	chr3:52002253-52002263
26	TAF1	chr3:52002209-52002568	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr3:52001408-52002328	NB4	blood:	n/a	n/a
28	TCF3	chr3:52002228-52002487	GM12878	blood:	n/a	chr3:52002351-52002367
29	POLR2A	chr3:52001322-52002351	HEK293	kidney:	n/a	n/a
30	TCF12	chr3:52002217-52002604	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:52000993-52002724	H1-neurons	neurons:	n/a	n/a
32	JUND	chr3:52002241-52002675	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:52000905-52002797	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr3:52001330-52002720	SK-N-SH	brain:	n/a	n/a
35	YY1	chr3:52002135-52002471	SK-N-SH_RA	brain:	n/a	n/a
36	GATA2	chr3:52001976-52002429	SH-SY5Y	brain:	n/a	chr3:52002158-52002167
37	POLR2A	chr3:52001100-52002469	HepG2	liver:	n/a	n/a
38	POLR2A	chr3:52001573-52002273	GM12892	blood:	n/a	n/a
39	POLR2A	chr3:52001184-52002480	MCF-7	breast:	n/a	n/a
40	MXI1	chr3:52000907-52002412	IMR90	lung:	n/a	n/a
41	POLR2A	chr3:52001050-52002378	HCT-116	colon:	n/a	n/a
42	MAX	chr3:52001771-52002524	SK-N-SH	brain:	n/a	chr3:52002253-52002263
43	POLR2A	chr3:52001489-52002308	K562	blood:	n/a	n/a
44	CHD2	chr3:52002249-52002449	GM12878	blood:	n/a	chr3:52002329-52002339
45	CHD2	chr3:52002123-52002659	H1-hESC	embryonic stem cell:	n/a	chr3:52002329-52002339
46	SIN3A	chr3:52001041-52002724	H1-hESC	embryonic stem cell:	n/a	chr3:52001042-52001056 chr3:52002033-52002046
47	MAX	chr3:52001743-52002645	H1-hESC	embryonic stem cell:	n/a	chr3:52002253-52002263
48	POLR2A	chr3:52001537-52002462	PANC-1	pancreas:	n/a	n/a
49	MAX	chr3:52001699-52002385	Hela-S3	cervix:	n/a	chr3:52002253-52002263
50	POLR2A	chr3:52001169-52003046	H1-hESC	embryonic stem cell:	n/a	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	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
8	chr3:51976428..51980212-chr3:52001978..52006587,6	MCF-7	breast:
9	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:

Variant related genes	Relation type
PCBP4	TF binding region
ABHD14A	TF binding region
ENSG00000145050	Chromatin interaction
ENSG00000180929	Chromatin interaction
ENSG00000041880	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:127 , 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	chr3:52000600-52002400	Active TSS	NHDF-Ad	bronchial
4	chr3:52000600-52002600	Active TSS	Brain Anterior Caudate	brain
5	chr3:52000800-52002400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:52000800-52002400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:52000800-52002400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr3:52000800-52002400	Active TSS	NHLF	lung
9	chr3:52000800-52002600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr3:52000800-52002600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:52000800-52002600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:52000800-52002600	Active TSS	A549	lung
13	chr3:52001000-52002400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:52001000-52002600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:52001000-52002600	Active TSS	Aorta	Aorta
16	chr3:52001200-52002400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:52001200-52002400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:52001200-52002400	Active TSS	Ovary	ovary
19	chr3:52001200-52002600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:52001200-52002600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr3:52001200-52002600	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr3:52001200-52002600	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:52001200-52002600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr3:52001200-52002600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:52001400-52002400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:52001600-52002400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:52001600-52002400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:52001600-52002400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr3:52001800-52002400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:52001800-52002600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:52001800-52002800	Flanking Active TSS	Dnd41	blood
32	chr3:52001800-52003200	Enhancers	Fetal Heart	heart
33	chr3:52001800-52007600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr3:52002000-52002400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:52002000-52002400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:52002000-52002400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:52002000-52002400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr3:52002000-52002400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:52002000-52002400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr3:52002000-52002400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr3:52002000-52002400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52002000-52002400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr3:52002000-52002400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr3:52002000-52002400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:52002000-52002400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr3:52002000-52002400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:52002000-52002400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr3:52002000-52002400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr3:52002000-52002400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:52002000-52002400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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