Variant report

Variant	rs538540417
Chromosome Location	chr3:133293300-133293301
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	USF1	chr3:133293069-133293784	HCT-116	colon:	n/a	chr3:133293251-133293262
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	FOXP2	chr3:133293100-133293362	PFSK-1	brain:	n/a	n/a
5	BCL3	chr3:133293060-133293605	GM12878	blood:	n/a	n/a
6	CTCF	chr3:133293279-133293487	Fibrobl	skin:	n/a	chr3:133293390-133293397 chr3:133293373-133293386
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	USF1	chr3:133293070-133293510	SK-N-SH_RA	brain:	n/a	chr3:133293251-133293262
11	POLR2A	chr3:133292270-133293804	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:133291583-133294198	HepG2	liver:	n/a	n/a
13	USF1	chr3:133293113-133293509	H1-hESC	embryonic stem cell:	n/a	chr3:133293251-133293262
14	MTA3	chr3:133293145-133294173	GM12878	blood:	n/a	n/a
15	TAF1	chr3:133293053-133293672	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr3:133293260-133293410	HA-sp	spinal cord:	n/a	chr3:133293390-133293397 chr3:133293373-133293386
17	NFATC1	chr3:133293127-133293792	GM12878	blood:	n/a	n/a
18	CTCF	chr3:133293300-133293480	GM12878	blood:	n/a	chr3:133293390-133293397 chr3:133293373-133293386
19	POLR2A	chr3:133291835-133293519	MCF-7	breast:	n/a	n/a
20	BCL11A	chr3:133293259-133293647	GM12878	blood:	n/a	n/a
21	MXI1	chr3:133291860-133294720	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:133292395-133293485	A549	lung:	n/a	n/a
23	POLR2A	chr3:133293060-133293790	HCT-116	colon:	n/a	n/a
24	POLR2A	chr3:133291771-133293822	GM12878	blood:	n/a	n/a
25	SIN3AK20	chr3:133293294-133293552	A549	lung:	n/a	n/a
26	USF1	chr3:133293006-133293590	HCT-116	colon:	n/a	chr3:133293251-133293262
27	MAX	chr3:133293046-133293681	A549	lung:	n/a	n/a
28	BRCA1	chr3:133293279-133293853	Hela-S3	cervix:	n/a	n/a
29	USF2	chr3:133293242-133293402	K562	blood:	n/a	chr3:133293251-133293262
30	EBF1	chr3:133293219-133294166	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:133291758-133293832	HUVEC	blood vessel:	n/a	n/a
32	CREB1	chr3:133293209-133293605	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr3:133293300-133293450	GM12866	blood:	n/a	chr3:133293390-133293397 chr3:133293373-133293386
34	POLR2A	chr3:133291012-133295811	GM12878	blood:	n/a	n/a
35	CHD1	chr3:133292466-133295357	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:133292377-133294515	GM12891	blood:	n/a	n/a
37	CCNT2	chr3:133291928-133293606	K562	blood:	n/a	chr3:133292264-133292273
38	POLR2A	chr3:133293034-133293831	GM12891	blood:	n/a	n/a
39	HEY1	chr3:133292328-133293912	K562	blood:	n/a	chr3:133292641-133292656 chr3:133292663-133292678 chr3:133292675-133292690 chr3:133292624-133292639
40	TCF12	chr3:133293206-133293556	GM12878	blood:	n/a	n/a
41	ATF3	chr3:133293083-133293387	H1-hESC	embryonic stem cell:	n/a	n/a
42	HCFC1	chr3:133293279-133293617	K562	blood:	n/a	n/a
43	USF1	chr3:133293127-133293473	A549	lung:	n/a	chr3:133293251-133293262
44	CTCF	chr3:133293300-133293450	GM12873	blood:	n/a	chr3:133293390-133293397 chr3:133293373-133293386
45	POLR2A	chr3:133291200-133293539	GM10847	blood:	n/a	n/a
46	POLR2A	chr3:133291624-133293945	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:133291780-133293897	Hela-S3	cervix:	n/a	n/a
48	MAX	chr3:133293030-133293528	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr3:133293260-133293410	GM12875	blood:	n/a	chr3:133293390-133293397 chr3:133293373-133293386
50	ELK1	chr3:133293288-133293660	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:65596825..65597694-chr3:133292711..133293433,2	Hela-S3	cervix:
2	chr3:133164640..133168534-chr3:133291750..133294077,5	MCF-7	breast:
3	chr21:38737416..38739692-chr3:133291408..133294289,2	MCF-7	breast:
4	chr3:133207179..133209818-chr3:133291516..133294111,3	MCF-7	breast:
5	chr3:132440102..132442906-chr3:133291126..133294877,5	K562	blood:
6	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
7	chr1:144533945..144534883-chr3:133292589..133293471,2	Hela-S3	cervix:
8	chr20:57467067..57467853-chr3:133292915..133293441,2	Hela-S3	cervix:
9	chr10:71930068..71930946-chr3:133292953..133293844,2	Hela-S3	cervix:
10	chr3:132439752..132442432-chr3:133291591..133294160,3	K562	blood:
11	chr19:47291403..47292001-chr3:133293045..133294029,2	NB4	blood:
12	chr3:133207094..133210649-chr3:133290648..133294454,4	MCF-7	breast:

Variant related genes	Relation type
CDV3	TF binding region
ENSG00000200156	Chromatin interaction
ENSG00000248724	Chromatin interaction
ENSG00000170819	Chromatin interaction
ENSG00000105281	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000273210	Chromatin interaction
ENSG00000079332	Chromatin interaction
ENSG00000087460	Chromatin interaction
ENSG00000113971	Chromatin interaction
ENSG00000214301	Chromatin interaction
ENSG00000157540	Chromatin interaction
ENSG00000249993	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:14 , 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
9	esv10255	chr3:133292719-133293670	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv591824	chr3:133292746-133293438	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
11	nsv591825	chr3:133292746-133293489	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
12	nsv591826	chr3:133292746-133293540	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
13	esv1800456	chr3:133292746-133294203	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
14	nsv591827	chr3:133292818-133293489	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	17 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	chr3:133291200-133294000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:133291400-133293800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:133291600-133293600	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:133291600-133293600	Active TSS	Brain Germinal Matrix	brain
5	chr3:133291600-133293600	Active TSS	Fetal Brain Female	brain
6	chr3:133291600-133293800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:133291600-133293800	Active TSS	Psoas Muscle	Psoas
8	chr3:133291600-133294000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:133291600-133294000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:133291600-133294000	Active TSS	Right Ventricle	heart
11	chr3:133291600-133294400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:133291600-133295000	Active TSS	Colonic Mucosa	Colon
13	chr3:133291600-133295000	Active TSS	Right Atrium	heart
14	chr3:133291800-133293400	Active TSS	Brain Hippocampus Middle	brain
15	chr3:133291800-133293600	Active TSS	Liver	Liver
16	chr3:133291800-133293800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr3:133291800-133293800	Active TSS	Fetal Stomach	stomach
18	chr3:133291800-133293800	Active TSS	Thymus	Thymus
19	chr3:133291800-133293800	Active TSS	A549	lung
20	chr3:133291800-133294000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:133291800-133294000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:133291800-133294000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:133291800-133294200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:133291800-133294200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:133291800-133294200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:133291800-133294200	Active TSS	Fetal Muscle Trunk	muscle
27	chr3:133291800-133294200	Active TSS	Ovary	ovary
28	chr3:133291800-133294200	Active TSS	Pancreas	Pancrea
29	chr3:133291800-133294800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:133291800-133295000	Active TSS	Left Ventricle	heart
31	chr3:133291800-133295400	Active TSS	Aorta	Aorta
32	chr3:133292000-133293400	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr3:133292000-133293400	Active TSS	Primary B cells from cord blood	blood
34	chr3:133292000-133293400	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:133292000-133293400	Weak transcription	Stomach Mucosa	stomach
36	chr3:133292000-133293600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:133292000-133293600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:133292000-133293600	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr3:133292000-133293600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:133292000-133293600	Active TSS	Adipose Nuclei	Adipose
41	chr3:133292000-133293600	Active TSS	Brain Anterior Caudate	brain
42	chr3:133292000-133293600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr3:133292000-133293600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:133292000-133293600	Active TSS	Brain Substantia Nigra	brain
45	chr3:133292000-133293600	Active TSS	Colon Smooth Muscle	Colon
46	chr3:133292000-133293600	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:133292000-133293600	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:133292000-133293600	Active TSS	GM12878-XiMat	blood
49	chr3:133292000-133293600	Active TSS	HSMM	muscle
50	chr3:133292000-133293600	Active TSS	NHDF-Ad	bronchial

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