Variant report

Variant	rs116498908
Chromosome Location	chr3:133291979-133291980
allele	C/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	chr3:133291520-133292988	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr3:133291165-133295546	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:133291837-133293023	H1-neurons	neurons:	n/a	n/a
4	MAX	chr3:133291743-133292841	SK-N-SH	brain:	n/a	n/a
5	MAX	chr3:133291743-133292747	MCF-7	breast:	n/a	n/a
6	PAX5	chr3:133291860-133292256	GM12878	blood:	n/a	n/a
7	YY1	chr3:133291793-133292066	GM12892	blood:	n/a	n/a
8	CTCF	chr3:133291900-133292050	GM12864	blood:	n/a	n/a
9	GATA1	chr3:133291194-133292335	PBDE	blood:	n/a	chr3:133291719-133291732 chr3:133291721-133291729 chr3:133291323-133291333 chr3:133291394-133291403
10	NFATC1	chr3:133291260-133292209	GM12878	blood:	n/a	n/a
11	BCLAF1	chr3:133291095-133292241	GM12878	blood:	n/a	chr3:133291906-133291915 chr3:133291421-133291429 chr3:133291396-133291405 chr3:133291503-133291512
12	POLR2A	chr3:133291159-133293723	HUVEC	blood vessel:	n/a	n/a
13	JUND	chr3:133290875-133293721	GM12878	blood:	n/a	chr3:133291396-133291404 chr3:133291395-133291405 chr3:133292292-133292303 chr3:133292374-133292383 chr3:133291395-133291405 chr3:133291397-133291404 chr3:133291396-133291404 chr3:133292333-133292342
14	IRF1	chr3:133291298-133292758	K562	blood:	n/a	chr3:133292260-133292274 chr3:133291496-133291513 chr3:133291704-133291713 chr3:133291502-133291512 chr3:133292350-133292364 chr3:133291395-133291404
15	GTF2F1	chr3:133291850-133292157	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr3:133291659-133292286	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:133291583-133294198	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:133291354-133293019	K562	blood:	n/a	n/a
19	SIN3AK20	chr3:133291769-133292057	A549	lung:	n/a	n/a
20	POLR2A	chr3:133291835-133293519	MCF-7	breast:	n/a	n/a
21	CHD2	chr3:133291191-133292830	GM12878	blood:	n/a	chr3:133292262-133292272 chr3:133292366-133292376
22	POLR2A	chr3:133291826-133292256	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:133291855-133292213	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr3:133291860-133294720	IMR90	lung:	n/a	n/a
25	POLR2A	chr3:133291771-133293822	GM12878	blood:	n/a	n/a
26	CEBPB	chr3:133291321-133292258	IMR90	lung:	n/a	chr3:133291668-133291681 chr3:133291668-133291681
27	SIN3AK20	chr3:133291862-133292201	SK-N-SH	brain:	n/a	n/a
28	NFYA	chr3:133291921-133292423	GM12878	blood:	n/a	chr3:133292331-133292346 chr3:133292331-133292346 chr3:133292334-133292344 chr3:133292202-133292217 chr3:133292201-133292213 chr3:133292202-133292217 chr3:133292202-133292216
29	FOS	chr3:133291288-133292339	HUVEC	blood vessel:	n/a	chr3:133291396-133291404 chr3:133291395-133291405 chr3:133292292-133292303 chr3:133291394-133291405 chr3:133291395-133291405 chr3:133291397-133291404 chr3:133291396-133291404
30	CTCF	chr3:133291932-133292374	GM12878	blood:	n/a	chr3:133292131-133292144 chr3:133292131-133292144
31	HCFC1	chr3:133291676-133292847	K562	blood:	n/a	n/a
32	STAT5A	chr3:133291183-133292209	GM12878	blood:	n/a	chr3:133291295-133291306
33	MAFK	chr3:133291605-133292319	HepG2	liver:	n/a	chr3:133291692-133291706
34	POLR2A	chr3:133291758-133293832	HUVEC	blood vessel:	n/a	n/a
35	SIN3AK20	chr3:133291937-133292181	HepG2	liver:	n/a	n/a
36	FOXA2	chr3:133291940-133292237	HepG2	liver:	n/a	n/a
37	E2F6	chr3:133291951-133292219	K562	blood:	n/a	chr3:133292105-133292114 chr3:133292204-133292213
38	POLR2A	chr3:133291692-133292197	K562	blood:	n/a	n/a
39	HEY1	chr3:133291830-133292224	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:133291012-133295811	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:133291234-133292240	GM12891	blood:	n/a	n/a
42	CCNT2	chr3:133291928-133293606	K562	blood:	n/a	chr3:133292264-133292273
43	NFYA	chr3:133291865-133292508	Hela-S3	cervix:	n/a	chr3:133292331-133292346 chr3:133292331-133292346 chr3:133292334-133292344 chr3:133292202-133292217 chr3:133292201-133292213 chr3:133292202-133292217 chr3:133292202-133292216
44	BHLHE40	chr3:133291893-133292162	HepG2	liver:	n/a	n/a
45	CEBPB	chr3:133291481-133292169	A549	lung:	n/a	chr3:133291668-133291681 chr3:133291668-133291681
46	MYC	chr3:133291930-133292844	MCF-7	breast:	n/a	n/a
47	MAFK	chr3:133291563-133292439	IMR90	lung:	n/a	chr3:133291692-133291706
48	POLR2A	chr3:133291200-133293539	GM10847	blood:	n/a	n/a
49	POLR2A	chr3:133291624-133293945	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:133291780-133293897	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:133291979-133292029	HAEpiC	amniotic membrane:	n/a
2	chr3:133291979-133292029	HL-60	blood:	n/a
3	chr3:133291979-133292029	HCT-116	colon:	n/a
4	chr3:133291979-133292029	H1-hESC	embryonic stem cell:	embryo
5	chr3:133291979-133292029	HCF	heart:	n/a
6	chr3:133291979-133292029	LNCaP	prostate:	n/a
7	chr3:133291979-133292029	AG04449	skin:	fetal
8	chr3:133291979-133292029	SK-N-SH	brain:	n/a
9	chr3:133291979-133292029	GM12891	blood:	n/a
10	chr3:133291979-133292029	GM06990	blood:	n/a
11	chr3:133291979-133292029	HRE	kidney:	n/a
12	chr3:133291979-133292029	AG09309	skin:	n/a
13	chr3:133291979-133292029	PFSK-1	brain:	n/a
14	chr3:133291979-133292029	AG09319	gingival:	n/a
15	chr3:133291979-133292029	SAEC	small airway:	n/a
16	chr3:133291979-133292029	HRCEpiC	kidney:	n/a
17	chr3:133291979-133292029	NT2-D1	testis:	n/a
18	chr3:133291979-133292029	SKMC	muscle:	n/a
19	chr3:133291979-133292029	ProgFib	skin:	n/a
20	chr3:133291979-133292029	K562	blood:	n/a
21	chr3:133291979-133292029	HCM	heart:	n/a
22	chr3:133291979-133292029	CMK	blood:	n/a
23	chr3:133291979-133292029	Hepatocyte	liver:	n/a
24	chr3:133291979-133292029	A549	lung:	n/a
25	chr3:133291979-133292029	AG04450	lung:	fetal
26	chr3:133291979-133292029	HMEC	breast:	n/a
27	chr3:133291979-133292029	SK-N-SH_RA	brain:	n/a
28	chr3:133291979-133292029	T-47D	breast:	n/a
29	chr3:133291979-133292029	HNPCEpiC	eye:	n/a
30	chr3:133291979-133292029	NHBE	bronchial:	n/a
31	chr3:133291979-133292029	NB4	blood:	n/a
32	chr3:133291979-133292029	HIPEpiC	eye:	n/a
33	chr3:133291979-133292029	ovcar-3	ovarian:	n/a
34	chr3:133291979-133292029	ECC-1	luminal epithelium:	n/a
35	chr3:133291979-133292029	HEEpiC	esophagus:	n/a
36	chr3:133291979-133292029	BE2_C	brain:	n/a
37	chr3:133291979-133292029	AG10803	skin:	n/a
38	chr3:133291979-133292029	PANC-1	pancreas:	n/a
39	chr3:133291979-133292029	Caco-2	colon:	n/a
40	chr3:133291979-133292029	HepG2	liver:	n/a
41	chr3:133291979-133292029	HCPEpiC	choroid plexus:	n/a
42	chr3:133291979-133292029	IMR90	lung:	fetal
43	chr3:133291979-133292029	MCF-7	breast:	n/a
44	chr3:133291979-133292029	SK-N-MC	brain:	n/a
45	chr3:133291979-133292029	NH-A	brain:	n/a
46	chr3:133291979-133292029	PrEC	prostate:	n/a
47	chr3:133291979-133292029	BJ	skin:	n/a
48	chr3:133291979-133292029	HUVEC	blood vessel:	n/a
49	chr3:133291979-133292029	RPTEC	kidney:	n/a
50	chr3:133291979-133292029	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:133164640..133168534-chr3:133291750..133294077,5	MCF-7	breast:
2	chr21:38737416..38739692-chr3:133291408..133294289,2	MCF-7	breast:
3	chr3:133207179..133209818-chr3:133291516..133294111,3	MCF-7	breast:
4	chr3:132440102..132442906-chr3:133291126..133294877,5	K562	blood:
5	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
6	chr3:132439752..132442432-chr3:133291591..133294160,3	K562	blood:
7	chr3:133207094..133210649-chr3:133290648..133294454,4	MCF-7	breast:
8	chr3:133287190..133289166-chr3:133290175..133292220,2	K562	blood:

Variant related genes	Relation type
CDV3	TF binding region
CDV3	CpG island
ENSG00000113971	Chromatin interaction
ENSG00000157540	Chromatin interaction
ENSG00000249993	Chromatin interaction
ENSG00000214301	Chromatin interaction
ENSG00000248724	Chromatin interaction
ENSG00000170819	Chromatin interaction
ENSG00000273210	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817019	chr3:133290960-133293461	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
2	nsv591821	chr3:133290960-133293591	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	esv3393233	chr3:133291062-133294360	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
4	esv3356701	chr3:133291487-133294035	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	esv3331679	chr3:133291512-133294210	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
6	esv3423184	chr3:133291787-133294635	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133288000-133292400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:133289400-133292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:133289600-133292400	Weak transcription	Esophagus	oesophagus
4	chr3:133289600-133292400	Weak transcription	Lung	lung
5	chr3:133289800-133292400	Weak transcription	Small Intestine	intestine
6	chr3:133289800-133293200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:133290800-133292000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr3:133290800-133292000	Flanking Active TSS	GM12878-XiMat	blood
9	chr3:133290800-133292000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:133290800-133292200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr3:133291000-133292000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr3:133291000-133292000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr3:133291000-133292000	Enhancers	Spleen	Spleen
14	chr3:133291000-133292200	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr3:133291000-133292200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr3:133291000-133292200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:133291000-133292200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:133291200-133292000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:133291200-133292000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:133291200-133292000	Enhancers	Stomach Mucosa	stomach
21	chr3:133291200-133292200	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr3:133291200-133292200	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr3:133291200-133292200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:133291200-133292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:133291200-133294000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:133291400-133292000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:133291400-133292000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:133291400-133292000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr3:133291400-133292000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr3:133291400-133292000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:133291400-133292000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr3:133291400-133292000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr3:133291400-133292000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:133291400-133292000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr3:133291400-133292000	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr3:133291400-133292000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr3:133291400-133292000	Flanking Active TSS	Hela-S3	cervix
38	chr3:133291400-133292000	Flanking Active TSS	HepG2	liver
39	chr3:133291400-133292000	Flanking Active TSS	NH-A	brain
40	chr3:133291400-133292200	Flanking Active TSS	Fetal Thymus	thymus
41	chr3:133291400-133292200	Flanking Active TSS	Dnd41	blood
42	chr3:133291400-133292200	Flanking Active TSS	K562	blood
43	chr3:133291400-133292400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:133291400-133293800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:133291600-133292000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
46	chr3:133291600-133292000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:133291600-133292000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr3:133291600-133292000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr3:133291600-133292000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:133291600-133292000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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