Variant report

Variant	rs540706431
Chromosome Location	chr3:133291280-133291281
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	chr3:133291165-133295546	GM12878	blood:	n/a	n/a
2	GATA1	chr3:133291194-133292335	PBDE	blood:	n/a	chr3:133291719-133291732 chr3:133291721-133291729 chr3:133291323-133291333 chr3:133291394-133291403
3	NFATC1	chr3:133291260-133292209	GM12878	blood:	n/a	n/a
4	BCLAF1	chr3:133291095-133292241	GM12878	blood:	n/a	chr3:133291906-133291915 chr3:133291421-133291429 chr3:133291396-133291405 chr3:133291503-133291512
5	POLR2A	chr3:133291159-133293723	HUVEC	blood vessel:	n/a	n/a
6	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
7	CHD2	chr3:133291191-133292830	GM12878	blood:	n/a	chr3:133292262-133292272 chr3:133292366-133292376
8	STAT5A	chr3:133291183-133292209	GM12878	blood:	n/a	chr3:133291295-133291306
9	POLR2A	chr3:133291012-133295811	GM12878	blood:	n/a	n/a
10	SPI1	chr3:133291242-133291575	GM12878	blood:	n/a	chr3:133291442-133291455 chr3:133291443-133291456
11	POLR2A	chr3:133291234-133292240	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:133291200-133293539	GM10847	blood:	n/a	n/a
13	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
14	MTA3	chr3:133291179-133292195	GM12878	blood:	n/a	n/a
15	EBF1	chr3:133291261-133292154	GM12878	blood:	n/a	chr3:133291515-133291526
16	YY1	chr3:133291176-133291626	K562	blood:	n/a	n/a
17	RELA	chr3:133291044-133292965	GM15510	blood:	n/a	n/a
18	MAFF	chr3:133291236-133292317	K562	blood:	n/a	chr3:133292153-133292171
19	SPI1	chr3:133291245-133291568	GM12878	blood:	n/a	chr3:133291442-133291455 chr3:133291443-133291456
20	BHLHE40	chr3:133291182-133293907	GM12878	blood:	n/a	chr3:133292670-133292686 chr3:133292636-133292652 chr3:133292628-133292644
21	POLR2A	chr3:133291102-133294602	GM12892	blood:	n/a	n/a
22	TBP	chr3:133291261-133292911	GM12878	blood:	n/a	n/a
23	FOXM1	chr3:133291022-133292799	GM12878	blood:	n/a	n/a
24	FOS	chr3:133291254-133292352	MCF10A-Er-Src	breast:	n/a	chr3:133291396-133291404 chr3:133291395-133291405 chr3:133292292-133292303 chr3:133291394-133291405 chr3:133291395-133291405 chr3:133291397-133291404 chr3:133291396-133291404 chr3:133292333-133292342
25	CTCF	chr3:133291160-133291310	GM12872	blood:	n/a	n/a
26	EP300	chr3:133291268-133292631	GM12878	blood:	n/a	chr3:133291444-133291458 chr3:133291929-133291943 chr3:133291445-133291454 chr3:133291395-133291404 chr3:133292373-133292382 chr3:133291426-133291440
27	RELA	chr3:133291203-133292704	GM19099	blood:	n/a	n/a
28	EBF1	chr3:133291232-133291760	GM12878	blood:	n/a	chr3:133291515-133291526
29	POU2F2	chr3:133291184-133291684	GM12878	blood:	n/a	chr3:133291484-133291494 chr3:133291485-133291493 chr3:133291481-133291494 chr3:133291480-133291498
30	NR2F2	chr3:133291156-133292579	K562	blood:	n/a	n/a
31	MAX	chr3:133291277-133293775	GM12878	blood:	n/a	n/a
32	TBL1XR1	chr3:133291075-133292831	GM12878	blood:	n/a	n/a
33	MAX	chr3:133291228-133293788	NB4	blood:	n/a	n/a
34	SPI1	chr3:133291270-133291504	K562	blood:	n/a	chr3:133291442-133291455 chr3:133291443-133291456
35	CTCF	chr3:133291180-133291330	HCPEpiC	choroid plexus:	n/a	n/a
36	POLR2A	chr3:133291080-133293758	GM19193	blood:	n/a	n/a
37	JUND	chr3:133291146-133292922	K562	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
38	CHD1	chr3:133291159-133295702	IMR90	lung:	n/a	chr3:133292262-133292272 chr3:133292366-133292376
39	RELA	chr3:133291212-133292813	GM10847	blood:	n/a	n/a
40	EP300	chr3:133291230-133292784	GM12878	blood:	n/a	chr3:133291444-133291458 chr3:133291929-133291943 chr3:133291445-133291454 chr3:133292663-133292679 chr3:133291395-133291404 chr3:133292373-133292382 chr3:133291426-133291440
41	MXI1	chr3:133291248-133294466	SK-N-SH	brain:	n/a	n/a
42	EP300	chr3:133291193-133292875	GM12878	blood:	n/a	chr3:133291444-133291458 chr3:133291929-133291943 chr3:133291445-133291454 chr3:133292663-133292679 chr3:133291395-133291404 chr3:133292373-133292382 chr3:133291426-133291440
43	JUND	chr3:133291140-133294676	SK-N-SH	brain:	n/a	chr3:133291396-133291404 chr3:133291395-133291405 chr3:133292292-133292303 chr3:133294325-133294334 chr3:133292374-133292383 chr3:133291395-133291405 chr3:133291397-133291404 chr3:133291396-133291404 chr3:133292333-133292342
44	POLR2A	chr3:133291185-133293761	GM18951	blood:	n/a	n/a
45	ETS1	chr3:133291185-133291616	GM12878	blood:	n/a	chr3:133291447-133291454
46	ZNF384	chr3:133290747-133292204	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:133291202-133294536	PBDE	blood:	n/a	n/a
48	STAT5A	chr3:133291144-133292310	GM12878	blood:	n/a	chr3:133291295-133291306 chr3:133292260-133292272
49	SPI1	chr3:133291195-133291582	HL-60	blood:	n/a	chr3:133291442-133291455 chr3:133291443-133291456
50	ATF2	chr3:133290917-133292593	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:132440102..132442906-chr3:133291126..133294877,5	K562	blood:
2	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
3	chr3:133207094..133210649-chr3:133290648..133294454,4	MCF-7	breast:
4	chr3:133287190..133289166-chr3:133290175..133292220,2	K562	blood:

Variant related genes	Relation type
CDV3	TF binding region
ENSG00000113971	Chromatin interaction
ENSG00000214301	Chromatin interaction
ENSG00000249993	Chromatin interaction
ENSG00000248724	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133285000-133291600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:133286600-133291800	Enhancers	HMEC	breast
3	chr3:133286800-133291600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:133287000-133291800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:133287000-133291800	Enhancers	HSMMtube	muscle
6	chr3:133287400-133291600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:133287800-133291400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:133287800-133291600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:133288000-133291400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:133288000-133291600	Enhancers	Osteobl	bone
11	chr3:133288000-133292400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:133289000-133291400	Weak transcription	Adipose Nuclei	Adipose
13	chr3:133289200-133291400	Weak transcription	Fetal Lung	lung
14	chr3:133289200-133291600	Enhancers	HUVEC	blood vessel
15	chr3:133289400-133291400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:133289400-133291400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:133289400-133291400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:133289400-133291600	Weak transcription	Right Atrium	heart
19	chr3:133289400-133292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:133289600-133291400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:133289600-133291400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:133289600-133291400	Enhancers	NH-A	brain
23	chr3:133289600-133291600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:133289600-133291600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:133289600-133291600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:133289600-133291600	Weak transcription	Fetal Intestine Large	intestine
27	chr3:133289600-133291600	Weak transcription	Psoas Muscle	Psoas
28	chr3:133289600-133292400	Weak transcription	Esophagus	oesophagus
29	chr3:133289600-133292400	Weak transcription	Lung	lung
30	chr3:133289800-133291400	Enhancers	K562	blood
31	chr3:133289800-133291800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:133289800-133292400	Weak transcription	Small Intestine	intestine
33	chr3:133289800-133293200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:133290000-133291400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:133290000-133291400	Weak transcription	HepG2	liver
36	chr3:133290000-133291600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:133290000-133291800	Weak transcription	Aorta	Aorta
38	chr3:133290000-133291800	Weak transcription	Left Ventricle	heart
39	chr3:133290200-133291400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:133290200-133291400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:133290200-133291600	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:133290400-133291400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:133290400-133291400	Weak transcription	A549	lung
44	chr3:133290600-133291400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:133290600-133291400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:133290600-133291400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:133290600-133291400	Enhancers	Fetal Thymus	thymus
48	chr3:133290600-133291400	Enhancers	Thymus	Thymus
49	chr3:133290600-133291800	Enhancers	Placenta	Placenta
50	chr3:133290800-133291400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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