Variant report

Variant	rs4687604
Chromosome Location	chr3:51975846-51975847
allele	A/G
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	SIN3AK20	chr3:51975610-51976498	HepG2	liver:	n/a	n/a
2	E2F6	chr3:51975754-51976595	A549	lung:	n/a	chr3:51976079-51976088 chr3:51976000-51976009 chr3:51976164-51976173 chr3:51976404-51976414
3	MAX	chr3:51975537-51976634	H1-hESC	embryonic stem cell:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
4	HCFC1	chr3:51974752-51977446	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr3:51975740-51975890	HVMF	connective:	n/a	n/a
6	RELA	chr3:51975696-51977084	GM18951	blood:	n/a	n/a
7	USF2	chr3:51975781-51976544	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAZ	chr3:51975614-51977420	Hela-S3	cervix:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
9	POLR2A	chr3:51975661-51976598	H1-neurons	neurons:	n/a	n/a
10	YY1	chr3:51975698-51975985	A549	lung:	n/a	chr3:51975944-51975955
11	IRF1	chr3:51975745-51976446	K562	blood:	n/a	chr3:51976075-51976089 chr3:51976038-51976052 chr3:51975996-51976010
12	HCFC1	chr3:51975763-51976705	K562	blood:	n/a	n/a
13	JUND	chr3:51975803-51975986	H1-hESC	embryonic stem cell:	n/a	n/a
14	ZNF263	chr3:51975715-51976838	HEK293-T-REx	kidney:	n/a	chr3:51976283-51976292
15	BRCA1	chr3:51975723-51976613	GM12878	blood:	n/a	n/a
16	YY1	chr3:51975676-51976464	GM12891	blood:	n/a	chr3:51976233-51976244 chr3:51975944-51975955
17	POLR2A	chr3:51975531-51977401	GM12892	blood:	n/a	n/a
18	MAZ	chr3:51975673-51977373	HepG2	liver:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
19	ZBTB7A	chr3:51975825-51976015	K562	blood:	n/a	n/a
20	POLR2A	chr3:51975668-51977272	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:51975721-51976067	A549	lung:	n/a	n/a
22	POLR2A	chr3:51975649-51976642	HL-60	blood:	n/a	n/a
23	USF1	chr3:51975785-51976502	SK-N-SH_RA	brain:	n/a	n/a
24	CEBPD	chr3:51975623-51975988	HepG2	liver:	n/a	n/a
25	GABPA	chr3:51975801-51976495	HepG2	liver:	n/a	chr3:51976163-51976177
26	MAX	chr3:51975542-51976773	ECC-1	luminal epithelium:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
27	TBP	chr3:51975827-51976574	GM12878	blood:	n/a	n/a
28	JUND	chr3:51975797-51976618	K562	blood:	n/a	n/a
29	MYBL2	chr3:51975749-51976866	HepG2	liver:	n/a	n/a
30	EP300	chr3:51975844-51976683	HepG2	liver:	n/a	n/a
31	MAX	chr3:51975393-51977389	Hela-S3	cervix:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
32	TAF1	chr3:51975711-51976522	Hela-S3	cervix:	n/a	n/a
33	HEY1	chr3:51975722-51976075	K562	blood:	n/a	chr3:51975943-51975958
34	POLR2A	chr3:51975727-51976018	SK-N-MC	brain:	n/a	n/a
35	RAD21	chr3:51975623-51977399	HCT-116	colon:	n/a	chr3:51976332-51976345 chr3:51976232-51976251 chr3:51976101-51976115 chr3:51976910-51976920
36	CTCF	chr3:51975796-51976496	Spleen_OC	spleen:	n/a	chr3:51976231-51976249 chr3:51976002-51976015 chr3:51975889-51975898 chr3:51976234-51976247 chr3:51976232-51976248
37	USF1	chr3:51975683-51976518	SK-N-SH_RA	brain:	n/a	n/a
38	NFYB	chr3:51975728-51976317	Hela-S3	cervix:	n/a	n/a
39	SP1	chr3:51975708-51976433	GM12878	blood:	n/a	chr3:51976041-51976051 chr3:51975999-51976008 chr3:51976077-51976089 chr3:51975998-51976010 chr3:51976077-51976089 chr3:51976078-51976092 chr3:51975999-51976013 chr3:51976041-51976051 chr3:51976078-51976087 chr3:51976000-51976009 chr3:51976079-51976088 chr3:51975998-51976010 chr3:51976077-51976088
40	MAX	chr3:51975685-51976331	H1-hESC	embryonic stem cell:	n/a	chr3:51975918-51975927
41	MAX	chr3:51975712-51976472	HUVEC	blood vessel:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
42	SP1	chr3:51975673-51976556	HepG2	liver:	n/a	chr3:51976041-51976051 chr3:51975999-51976008 chr3:51976077-51976089 chr3:51975998-51976010 chr3:51976077-51976089 chr3:51976078-51976092 chr3:51975999-51976013 chr3:51976041-51976051 chr3:51976078-51976087 chr3:51976000-51976009 chr3:51976079-51976088 chr3:51975998-51976010 chr3:51976077-51976088
43	USF1	chr3:51975708-51976045	A549	lung:	n/a	n/a
44	IRF3	chr3:51975841-51976218	GM12878	blood:	n/a	chr3:51976075-51976089 chr3:51976038-51976052 chr3:51975996-51976010
45	GABPA	chr3:51975798-51976440	H1-hESC	embryonic stem cell:	n/a	chr3:51976163-51976177
46	POLR2A	chr3:51975658-51976099	U87	brain:	n/a	n/a
47	POLR2A	chr3:51975643-51977304	GM19099	blood:	n/a	n/a
48	MYC	chr3:51975736-51976617	K562	blood:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
49	RCOR1	chr3:51975699-51976461	HepG2	liver:	n/a	n/a
50	USF1	chr3:51975731-51976174	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51975062..51978431-chr3:52015984..52020263,5	K562	blood:
2	chr3:51975614..51976314-chr5:43120889..43121451,2	Hela-S3	cervix:
3	chr3:51974812..51978768-chr3:52006594..52010604,6	MCF-7	breast:
4	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
5	chr3:51974226..51977659-chr3:52020694..52024166,4	K562	blood:
6	chr3:51974734..51977966-chr3:52006518..52010028,6	MCF-7	breast:
7	chr3:51975804..51978871-chr3:52028445..52030301,4	K562	blood:
8	chr16:30076382..30077075-chr3:51975737..51976462,2	Hela-S3	cervix:
9	chr3:51974644..51978429-chr3:52029121..52032128,7	MCF-7	breast:
10	chr3:51862209..51864973-chr3:51975409..51978321,2	MCF-7	breast:
11	chr3:51975412..51976037-chr8:145013507..145014372,2	Hela-S3	cervix:
12	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
13	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
14	chr3:51974725..51977771-chr3:52005335..52009465,8	K562	blood:
15	chr3:51975816..51976930-chr3:52016726..52017409,3	Hela-S3	cervix:
16	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
17	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:
18	chr3:51974392..51977854-chr3:52027120..52030701,3	MCF-7	breast:
19	chr3:51975763..51976713-chr3:52007592..52008460,5	K562	blood:
20	chr1:45186750..45187594-chr3:51975747..51976594,2	HCT-116	colon:
21	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:
22	chr3:51975782..51976919-chr3:52007634..52008466,4	MCF-7	breast:
23	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:
24	chr3:51975678..51978117-chr3:52018353..52021936,3	MCF-7	breast:
25	chr3:51975795..51976454-chr3:52007861..52008453,3	MCF-7	breast:

Variant related genes	Relation type
PARP3	TF binding region
ENSG00000248487	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000229972	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000272762	Chromatin interaction
ENSG00000164086	Chromatin interaction
ENSG00000178209	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000149925	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11707276	1.00[MEX][hapmap]
rs12632925	1.00[CHD][hapmap]
rs178919	1.00[LWK][hapmap]
rs34821455	1.00[CHD][hapmap]
rs7426999	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv590280	chr3:51967439-51978327	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
8	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
9	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51974400-51976000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:51974400-51976400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:51974400-51976400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:51974400-51976400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:51974400-51976400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr3:51974600-51976000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:51974600-51976600	Active TSS	A549	lung
8	chr3:51974600-51976800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr3:51974800-51976200	Active TSS	NHLF	lung
10	chr3:51974800-51976600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr3:51974800-51976600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:51974800-51976600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr3:51975000-51976000	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr3:51975000-51976400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:51975000-51976400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:51975000-51976400	Active TSS	GM12878-XiMat	blood
17	chr3:51975000-51976400	Active TSS	NHDF-Ad	bronchial
18	chr3:51975000-51976600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:51975000-51976600	Active TSS	Lung	lung
20	chr3:51975000-51976800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr3:51975000-51976800	Active TSS	Small Intestine	intestine
22	chr3:51975200-51976000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:51975200-51976000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:51975200-51976200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:51975200-51976200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:51975200-51976200	Active TSS	HMEC	breast
27	chr3:51975200-51976400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:51975200-51976400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:51975200-51976400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:51975200-51976400	Active TSS	Fetal Intestine Large	intestine
31	chr3:51975200-51976400	Active TSS	K562	blood
32	chr3:51975200-51976600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:51975200-51976600	Active TSS	Ovary	ovary
34	chr3:51975200-51977400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr3:51975400-51976000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:51975400-51976200	Active TSS	NH-A	brain
37	chr3:51975400-51976400	Active TSS	H1 Cell Line	embryonic stem cell
38	chr3:51975400-51976400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:51975400-51976400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:51975400-51976400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:51975400-51976400	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr3:51975400-51976400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:51975400-51976400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr3:51975400-51976400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:51975400-51976400	Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:51975400-51976400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:51975400-51976400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:51975400-51976400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr3:51975400-51976400	Active TSS	Fetal Intestine Small	intestine
50	chr3:51975400-51976400	Active TSS	Fetal Kidney	kidney

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