Variant report

Variant	rs542459749
Chromosome Location	chr3:133292376-133292377
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	chr3:133292311-133293535	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:133291837-133293023	H1-neurons	neurons:	n/a	n/a
5	MAX	chr3:133291743-133292841	SK-N-SH	brain:	n/a	n/a
6	MAX	chr3:133291743-133292747	MCF-7	breast:	n/a	n/a
7	PAX5	chr3:133292354-133293485	GM12892	blood:	n/a	chr3:133292514-133292523
8	POLR2A	chr3:133291159-133293723	HUVEC	blood vessel:	n/a	n/a
9	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
10	PML	chr3:133292339-133292696	K562	blood:	n/a	n/a
11	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
12	POLR2A	chr3:133292270-133293804	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:133291583-133294198	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:133291354-133293019	K562	blood:	n/a	n/a
15	POLR2A	chr3:133291835-133293519	MCF-7	breast:	n/a	n/a
16	CHD2	chr3:133291191-133292830	GM12878	blood:	n/a	chr3:133292262-133292272 chr3:133292366-133292376
17	POLR2A	chr3:133292348-133292995	K562	blood:	n/a	n/a
18	MXI1	chr3:133291860-133294720	IMR90	lung:	n/a	n/a
19	POLR2A	chr3:133291771-133293822	GM12878	blood:	n/a	n/a
20	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
21	HCFC1	chr3:133291676-133292847	K562	blood:	n/a	n/a
22	POLR2A	chr3:133291758-133293832	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr3:133291012-133295811	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:133292360-133292945	HepG2	liver:	n/a	n/a
25	CCNT2	chr3:133291928-133293606	K562	blood:	n/a	chr3:133292264-133292273
26	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
27	HEY1	chr3:133292328-133293912	K562	blood:	n/a	chr3:133292641-133292656 chr3:133292663-133292678 chr3:133292675-133292690 chr3:133292624-133292639
28	MYC	chr3:133291930-133292844	MCF-7	breast:	n/a	n/a
29	POLR2A	chr3:133292324-133293045	HepG2	liver:	n/a	n/a
30	MAFK	chr3:133291563-133292439	IMR90	lung:	n/a	chr3:133291692-133291706
31	POLR2A	chr3:133291200-133293539	GM10847	blood:	n/a	n/a
32	POLR2A	chr3:133291624-133293945	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:133291780-133293897	Hela-S3	cervix:	n/a	n/a
34	POU2F2	chr3:133290845-133293004	GM12878	blood:	n/a	chr3:133292242-133292252 chr3:133292242-133292252 chr3:133292243-133292253 chr3:133291484-133291494 chr3:133292243-133292254 chr3:133291485-133291493 chr3:133292238-133292259 chr3:133292237-133292259 chr3:133292239-133292257 chr3:133291481-133291494 chr3:133292244-133292252 chr3:133291480-133291498
35	CREB1	chr3:133291973-133292516	ECC-1	luminal epithelium:	n/a	n/a
36	SP1	chr3:133291898-133292538	H1-hESC	embryonic stem cell:	n/a	chr3:133292262-133292274 chr3:133292179-133292190 chr3:133292263-133292272 chr3:133292263-133292272 chr3:133292263-133292277 chr3:133292324-133292345 chr3:133292264-133292273 chr3:133292353-133292367 chr3:133292265-133292278 chr3:133292281-133292293 chr3:133292203-133292224 chr3:133292281-133292293
37	POLR2A	chr3:133291469-133294517	IMR90	lung:	n/a	n/a
38	RELA	chr3:133291044-133292965	GM15510	blood:	n/a	n/a
39	POLR2A	chr3:133291399-133292985	PFSK-1	brain:	n/a	n/a
40	POU2F2	chr3:133291785-133292433	GM12878	blood:	n/a	chr3:133292242-133292252 chr3:133292242-133292252 chr3:133292243-133292253 chr3:133292243-133292254 chr3:133292238-133292259 chr3:133292237-133292259 chr3:133292239-133292257 chr3:133292244-133292252
41	BHLHE40	chr3:133291182-133293907	GM12878	blood:	n/a	chr3:133292670-133292686 chr3:133292636-133292652 chr3:133292628-133292644
42	POLR2A	chr3:133292289-133293031	ECC-1	luminal epithelium:	n/a	n/a
43	FOS	chr3:133292037-133292394	MCF10A-Er-Src	breast:	n/a	chr3:133292292-133292303 chr3:133292374-133292383 chr3:133292333-133292342
44	POLR2A	chr3:133291102-133294602	GM12892	blood:	n/a	n/a
45	BRCA1	chr3:133291829-133292903	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:133291832-133293577	K562	blood:	n/a	n/a
47	NFYB	chr3:133291946-133292492	GM12878	blood:	n/a	chr3:133292331-133292346 chr3:133292199-133292214 chr3:133292331-133292346 chr3:133292334-133292344 chr3:133292202-133292217 chr3:133292201-133292213 chr3:133292202-133292217 chr3:133292202-133292216
48	TBP	chr3:133291261-133292911	GM12878	blood:	n/a	n/a
49	RCOR1	chr3:133291673-133292800	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:133291829-133293576	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:133292376-133292426	SK-N-MC	brain:	n/a
2	chr3:133292373-133292423	HCF	heart:	n/a
3	chr3:133292373-133292423	SK-N-MC	brain:	n/a
4	chr3:133292376-133292426	HCT-116	colon:	n/a
5	chr3:133292373-133292423	GM12891	blood:	n/a
6	chr3:133292376-133292426	Hela-S3	cervix:	n/a
7	chr3:133292376-133292426	AG04450	lung:	fetal
8	chr3:133292373-133292423	BJ	skin:	n/a
9	chr3:133292376-133292426	GM19239	blood:	n/a
10	chr3:133292373-133292423	PrEC	prostate:	n/a
11	chr3:133292376-133292426	PrEC	prostate:	n/a
12	chr3:133292373-133292423	GM12878	blood:	n/a
13	chr3:133292373-133292423	GM12892	blood:	n/a
14	chr3:133292373-133292423	T-47D	breast:	n/a
15	chr3:133292373-133292423	HCT-116	colon:	n/a
16	chr3:133292373-133292423	NHDF-neo	bronchial:	n/a
17	chr3:133292376-133292426	HCF	heart:	n/a
18	chr3:133292373-133292423	NH-A	brain:	n/a
19	chr3:133292373-133292423	Caco-2	colon:	n/a
20	chr3:133292373-133292423	NHBE	bronchial:	n/a
21	chr3:133292376-133292426	NHDF-neo	bronchial:	n/a
22	chr3:133292376-133292426	AG09319	gingival:	n/a
23	chr3:133292373-133292423	CMK	blood:	n/a
24	chr3:133292376-133292426	AG09309	skin:	n/a
25	chr3:133292373-133292423	HPAEpiC	pulmonary alveolar:	n/a
26	chr3:133292373-133292423	H1-hESC	embryonic stem cell:	embryo
27	chr3:133292373-133292423	HRE	kidney:	n/a
28	chr3:133292373-133292423	GM06990	blood:	n/a
29	chr3:133292376-133292426	K562	blood:	n/a
30	chr3:133292373-133292423	HCM	heart:	n/a
31	chr3:133292373-133292423	HCPEpiC	choroid plexus:	n/a
32	chr3:133292373-133292423	HUVEC	blood vessel:	n/a
33	chr3:133292376-133292426	IMR90	lung:	fetal
34	chr3:133292373-133292423	NT2-D1	testis:	n/a
35	chr3:133292373-133292423	K562	blood:	n/a
36	chr3:133292376-133292426	PANC-1	pancreas:	n/a
37	chr3:133292376-133292426	BJ	skin:	n/a
38	chr3:133292373-133292423	Hela-S3	cervix:	n/a
39	chr3:133292373-133292423	SKMC	muscle:	n/a
40	chr3:133292373-133292423	ECC-1	luminal epithelium:	n/a
41	chr3:133292376-133292426	NB4	blood:	n/a
42	chr3:133292373-133292423	LNCaP	prostate:	n/a
43	chr3:133292376-133292426	HCM	heart:	n/a
44	chr3:133292373-133292423	HepG2	liver:	n/a
45	chr3:133292373-133292423	HAEpiC	amniotic membrane:	n/a
46	chr3:133292373-133292423	AoSMC	blood vessel:	n/a
47	chr3:133292376-133292426	GM12892	blood:	n/a
48	chr3:133292373-133292423	SK-N-SH	brain:	n/a
49	chr3:133292373-133292423	GM19239	blood:	n/a
50	chr3:133292373-133292423	MCF-7	breast:	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	chr12:123380262..123380795-chr3:133292200..133293035,2	Hela-S3	cervix:
7	chr3:132439752..132442432-chr3:133291591..133294160,3	K562	blood:
8	chr3:133207094..133210649-chr3:133290648..133294454,4	MCF-7	breast:
9	chr3:133292322..133293201-chr3:142314859..142315610,2	HCT-116	colon:

Variant related genes	Relation type
CDV3	TF binding region
CDV3	CpG island
ENSG00000273210	Chromatin interaction
ENSG00000249993	Chromatin interaction
ENSG00000157540	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000214301	Chromatin interaction
ENSG00000170819	Chromatin interaction
ENSG00000248724	Chromatin interaction
ENSG00000113971	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv591822	chr3:133292102-133293489	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
8	nsv591823	chr3:133292102-133293618	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats	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	chr3:133291200-133292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:133291200-133294000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:133291400-133292400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:133291400-133293800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:133291600-133293600	Active TSS	Brain Cingulate Gyrus	brain
12	chr3:133291600-133293600	Active TSS	Brain Germinal Matrix	brain
13	chr3:133291600-133293600	Active TSS	Fetal Brain Female	brain
14	chr3:133291600-133293800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:133291600-133293800	Active TSS	Psoas Muscle	Psoas
16	chr3:133291600-133294000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:133291600-133294000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr3:133291600-133294000	Active TSS	Right Ventricle	heart
19	chr3:133291600-133294400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:133291600-133295000	Active TSS	Colonic Mucosa	Colon
21	chr3:133291600-133295000	Active TSS	Right Atrium	heart
22	chr3:133291800-133293400	Active TSS	Brain Hippocampus Middle	brain
23	chr3:133291800-133293600	Active TSS	Liver	Liver
24	chr3:133291800-133293800	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr3:133291800-133293800	Active TSS	Fetal Stomach	stomach
26	chr3:133291800-133293800	Active TSS	Thymus	Thymus
27	chr3:133291800-133293800	Active TSS	A549	lung
28	chr3:133291800-133294000	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:133291800-133294000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:133291800-133294000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:133291800-133294200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:133291800-133294200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:133291800-133294200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:133291800-133294200	Active TSS	Fetal Muscle Trunk	muscle
35	chr3:133291800-133294200	Active TSS	Ovary	ovary
36	chr3:133291800-133294200	Active TSS	Pancreas	Pancrea
37	chr3:133291800-133294800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:133291800-133295000	Active TSS	Left Ventricle	heart
39	chr3:133291800-133295400	Active TSS	Aorta	Aorta
40	chr3:133292000-133292400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:133292000-133292400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:133292000-133292400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:133292000-133292600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:133292000-133293200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr3:133292000-133293200	Weak transcription	Fetal Heart	heart
46	chr3:133292000-133293400	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:133292000-133293400	Active TSS	Primary B cells from cord blood	blood
48	chr3:133292000-133293400	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:133292000-133293400	Weak transcription	Stomach Mucosa	stomach
50	chr3:133292000-133293600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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