Variant report

Variant	rs371724415
Chromosome Location	chr4:48342928-48342929
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	JUN	chr4:48342560-48343706	K562	blood:	n/a	chr4:48342747-48342758 chr4:48342726-48342735 chr4:48343389-48343398 chr4:48343239-48343248
2	SP1	chr4:48342819-48343845	HCT-116	colon:	n/a	chr4:48343387-48343396 chr4:48343341-48343350 chr4:48343361-48343370 chr4:48343176-48343186 chr4:48343340-48343352 chr4:48343360-48343372 chr4:48343387-48343401 chr4:48343360-48343372 chr4:48343388-48343397 chr4:48343236-48343248 chr4:48343361-48343370 chr4:48343176-48343186 chr4:48343362-48343371 chr4:48343386-48343398 chr4:48343342-48343351 chr4:48343237-48343246 chr4:48343236-48343248 chr4:48343361-48343371 chr4:48343386-48343398 chr4:48343341-48343350 chr4:48343387-48343396
3	SIN3A	chr4:48342884-48344017	GM12878	blood:	n/a	chr4:48343390-48343401 chr4:48343422-48343431 chr4:48343093-48343104
4	ELF1	chr4:48342912-48343945	K562	blood:	n/a	chr4:48343238-48343250
5	POLR2A	chr4:48342918-48344085	GM12891	blood:	n/a	n/a
6	CUX1	chr4:48342784-48343240	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:48342228-48344387	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:48342702-48344406	HUVEC	blood vessel:	n/a	n/a
9	BHLHE40	chr4:48342757-48343684	GM12878	blood:	n/a	chr4:48343422-48343438 chr4:48343391-48343407 chr4:48343576-48343592 chr4:48343424-48343440
10	RFX5	chr4:48342863-48343750	Hela-S3	cervix:	n/a	n/a
11	E2F4	chr4:48342908-48343712	MCF10A-Er-Src	breast:	n/a	chr4:48343404-48343414 chr4:48343238-48343247
12	PML	chr4:48342508-48344642	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:48342886-48343364	GM12891	blood:	n/a	n/a
14	POLR2A	chr4:48342903-48343803	HCT-116	colon:	n/a	n/a
15	POLR2A	chr4:48342462-48343728	K562	blood:	n/a	n/a
16	UBTF	chr4:48342320-48345277	K562	blood:	n/a	n/a
17	POLR2A	chr4:48342893-48344029	GM12878	blood:	n/a	n/a
18	KAP1	chr4:48342302-48343261	U2OS	brain:	n/a	n/a
19	POLR2A	chr4:48342555-48344209	MCF10A-Er-Src	breast:	n/a	n/a
20	NR2F2	chr4:48342426-48343797	K562	blood:	n/a	n/a
21	POLR2A	chr4:48342315-48344444	IMR90	lung:	n/a	n/a
22	SIN3A	chr4:48342275-48344914	H1-hESC	embryonic stem cell:	n/a	chr4:48344167-48344178 chr4:48343390-48343401 chr4:48343422-48343431 chr4:48344167-48344180 chr4:48343093-48343104
23	ELK1	chr4:48342885-48343608	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr4:48342498-48344353	PFSK-1	brain:	n/a	n/a
25	RUNX3	chr4:48342646-48343804	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:48342366-48344589	K562	blood:	n/a	n/a
27	TAF1	chr4:48342843-48344341	ECC-1	luminal epithelium:	n/a	n/a
28	GABPA	chr4:48342745-48343771	HL-60	blood:	n/a	chr4:48343238-48343247 chr4:48343552-48343566
29	FOXA1	chr4:48342651-48343280	HepG2	liver:	n/a	n/a
30	TAF1	chr4:48342895-48343814	K562	blood:	n/a	n/a
31	TBP	chr4:48342551-48343291	Hela-S3	cervix:	n/a	n/a
32	TBL1XR1	chr4:48342854-48343304	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr4:48342722-48343332	K562	blood:	n/a	n/a
34	POLR2A	chr4:48342911-48344163	GM12878	blood:	n/a	n/a
35	REST	chr4:48342897-48343365	HepG2	liver:	n/a	n/a
36	POLR2A	chr4:48342593-48343788	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr4:48342751-48343810	GM12878	blood:	n/a	n/a
38	PML	chr4:48342370-48344072	K562	blood:	n/a	n/a
39	CHD1	chr4:48342148-48345930	IMR90	lung:	n/a	n/a
40	YY1	chr4:48342893-48344318	K562	blood:	n/a	chr4:48343494-48343516 chr4:48343239-48343250 chr4:48343506-48343516 chr4:48343512-48343523 chr4:48343499-48343518 chr4:48343507-48343515
41	POLR2A	chr4:48342681-48344532	HL-60	blood:	n/a	n/a
42	MYC	chr4:48342295-48343743	NB4	blood:	n/a	n/a
43	RAD21	chr4:48342492-48344680	IMR90	lung:	n/a	chr4:48343576-48343589 chr4:48343424-48343438 chr4:48343397-48343411
44	ZBTB7A	chr4:48342888-48343806	ECC-1	luminal epithelium:	n/a	chr4:48343324-48343331
45	CTCF	chr4:48342780-48342930	NHDF-neo	bronchial:	n/a	n/a
46	ARID3A	chr4:48342653-48343056	K562	blood:	n/a	n/a
47	MXI1	chr4:48342390-48345427	SK-N-SH	brain:	n/a	n/a
48	UBTF	chr4:48342477-48344421	K562	blood:	n/a	n/a
49	MAFF	chr4:48342861-48343275	HepG2	liver:	n/a	n/a
50	POLR2A	chr4:48342808-48344488	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:79479311..79479820-chr4:48342792..48343547,2	Hela-S3	cervix:
2	chr4:48342222..48343122-chr6:10417159..10417982,2	Hela-S3	cervix:
3	chr4:48341542..48343650-chr4:48378558..48381453,2	K562	blood:
4	chr4:48339667..48343042-chr4:48377720..48381453,4	K562	blood:
5	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
6	chr4:48341515..48344236-chr4:48506268..48509029,2	K562	blood:
7	chr2:96873883..96874519-chr4:48342610..48343559,2	NB4	blood:
8	chr4:48341290..48343185-chr4:52708590..52710145,2	K562	blood:
9	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
10	chr3:42641898..42642685-chr4:48342789..48343555,2	Hela-S3	cervix:
11	chr4:48269261..48273807-chr4:48342628..48344865,6	K562	blood:
12	chr4:48341909..48343469-chr4:48483589..48486077,2	K562	blood:

Variant related genes	Relation type
SLAIN2	TF binding region
ENSG00000114857	Chromatin interaction
ENSG00000137203	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000109171	Chromatin interaction
ENSG00000109184	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000145248	Chromatin interaction
ENSG00000135605	Chromatin interaction
ENSG00000075539	Chromatin interaction
ENSG00000184009	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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3377721	chr4:48342220-48345068	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48342000-48343000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr4:48342000-48343000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr4:48342000-48345400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:48342000-48345400	Active TSS	Fetal Intestine Large	intestine
5	chr4:48342000-48345600	Active TSS	Fetal Intestine Small	intestine
6	chr4:48342200-48343000	Flanking Active TSS	HUVEC	blood vessel
7	chr4:48342200-48343000	Flanking Active TSS	NHEK	skin
8	chr4:48342200-48343200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:48342200-48343200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:48342200-48343200	Flanking Active TSS	GM12878-XiMat	blood
11	chr4:48342200-48343600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:48342200-48344200	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr4:48342200-48344400	Active TSS	Colonic Mucosa	Colon
14	chr4:48342200-48344600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr4:48342200-48345200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr4:48342200-48345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:48342200-48345200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:48342200-48345200	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr4:48342200-48345400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:48342200-48345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:48342200-48345400	Active TSS	Brain Anterior Caudate	brain
22	chr4:48342200-48345600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr4:48342200-48345800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:48342400-48343000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr4:48342400-48343000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr4:48342400-48343000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:48342400-48343000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr4:48342400-48343000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr4:48342400-48343200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr4:48342400-48343200	Active TSS	Fetal Brain Male	brain
31	chr4:48342400-48343400	Active TSS	Right Atrium	heart
32	chr4:48342400-48344400	Active TSS	Brain Cingulate Gyrus	brain
33	chr4:48342400-48344400	Active TSS	Brain Substantia Nigra	brain
34	chr4:48342400-48344800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr4:48342400-48344800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:48342400-48344800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:48342400-48344800	Active TSS	Brain Hippocampus Middle	brain
38	chr4:48342400-48344800	Active TSS	Esophagus	oesophagus
39	chr4:48342400-48345000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:48342400-48345000	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr4:48342400-48345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:48342400-48345000	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr4:48342400-48345200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:48342400-48345200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:48342400-48345200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:48342400-48345200	Active TSS	Brain Angular Gyrus	brain
47	chr4:48342400-48345200	Active TSS	Colon Smooth Muscle	Colon
48	chr4:48342400-48345200	Active TSS	Fetal Muscle Trunk	muscle
49	chr4:48342400-48345200	Active TSS	Left Ventricle	heart
50	chr4:48342400-48345400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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