Variant report

Variant	rs560058387
Chromosome Location	chr4:56262142-56262143
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	JUND	chr4:56261910-56262306	A549	lung:	n/a	chr4:56262050-56262059
2	GABPA	chr4:56261937-56262696	H1-hESC	embryonic stem cell:	n/a	chr4:56262067-56262076
3	MAFK	chr4:56261482-56262274	Hela-S3	cervix:	n/a	n/a
4	SP1	chr4:56261772-56262261	A549	lung:	n/a	chr4:56262047-56262068 chr4:56262085-56262099
5	POLR2A	chr4:56261620-56262356	A549	lung:	n/a	n/a
6	E2F4	chr4:56261555-56262236	MCF10A-Er-Src	breast:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262136-56262146
7	MAX	chr4:56261475-56262910	HepG2	liver:	n/a	chr4:56261670-56261680
8	MYBL2	chr4:56261968-56262460	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:56261418-56262619	PFSK-1	brain:	n/a	n/a
10	MAX	chr4:56261350-56262354	MCF-7	breast:	n/a	chr4:56261670-56261680
11	YY1	chr4:56261565-56262808	GM12878	blood:	n/a	chr4:56262663-56262674 chr4:56262248-56262257 chr4:56262166-56262177 chr4:56262243-56262254 chr4:56261904-56261918 chr4:56262246-56262257 chr4:56262245-56262254
12	E2F4	chr4:56261590-56262783	K562	blood:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262243-56262253 chr4:56262136-56262146 chr4:56262246-56262256
13	POLR2A	chr4:56261604-56262358	HCT-116	colon:	n/a	n/a
14	HEY1	chr4:56261581-56262393	K562	blood:	n/a	chr4:56262325-56262340 chr4:56262103-56262118 chr4:56261904-56261919
15	MXI1	chr4:56260947-56266145	SK-N-SH	brain:	n/a	n/a
16	SIN3AK20	chr4:56261474-56262514	MCF-7	breast:	n/a	n/a
17	RAD21	chr4:56261464-56262288	IMR90	lung:	n/a	n/a
18	POLR2A	chr4:56261568-56262455	HCT-116	colon:	n/a	n/a
19	E2F4	chr4:56261967-56262220	GM12878	blood:	n/a	chr4:56262136-56262146
20	TCF12	chr4:56261960-56262319	GM12878	blood:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
21	POLR2A	chr4:56261482-56262483	U87	brain:	n/a	n/a
22	TCF12	chr4:56261565-56262891	ECC-1	luminal epithelium:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
23	YY1	chr4:56261630-56262335	ECC-1	luminal epithelium:	n/a	chr4:56262248-56262257 chr4:56262166-56262177 chr4:56262243-56262254 chr4:56261904-56261918 chr4:56262246-56262257 chr4:56262245-56262254
24	MAX	chr4:56261385-56262415	A549	lung:	n/a	chr4:56261670-56261680
25	BHLHE40	chr4:56261891-56262345	HepG2	liver:	n/a	n/a
26	POLR2A	chr4:56261662-56262375	HEK293	kidney:	n/a	n/a
27	POLR2A	chr4:56261613-56262500	ECC-1	luminal epithelium:	n/a	n/a
28	CEBPD	chr4:56262002-56262309	HepG2	liver:	n/a	n/a
29	NFYB	chr4:56261797-56262231	Hela-S3	cervix:	n/a	chr4:56262046-56262061 chr4:56262046-56262060 chr4:56262043-56262058 chr4:56262046-56262061
30	TBP	chr4:56261474-56262301	GM12878	blood:	n/a	n/a
31	IRF1	chr4:56261495-56262351	K562	blood:	n/a	n/a
32	TAF1	chr4:56261625-56262821	HepG2	liver:	n/a	n/a
33	TAF1	chr4:56261651-56262352	PFSK-1	brain:	n/a	n/a
34	EP300	chr4:56261563-56262485	ECC-1	luminal epithelium:	n/a	chr4:56262323-56262339 chr4:56262247-56262256 chr4:56262136-56262145 chr4:56261845-56261859 chr4:56262313-56262322 chr4:56262192-56262208 chr4:56262244-56262253
35	CREB1	chr4:56261492-56262464	GM12878	blood:	n/a	chr4:56261747-56261760
36	ZEB1	chr4:56261454-56262885	HepG2	liver:	n/a	n/a
37	TAF1	chr4:56261773-56262379	A549	lung:	n/a	n/a
38	YY1	chr4:56262004-56262276	A549	lung:	n/a	chr4:56262248-56262257 chr4:56262166-56262177 chr4:56262243-56262254 chr4:56262246-56262257 chr4:56262245-56262254
39	MAX	chr4:56261507-56262208	A549	lung:	n/a	chr4:56261670-56261680
40	TCF12	chr4:56261674-56262425	A549	lung:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
41	HMGN3	chr4:56261567-56263107	K562	blood:	n/a	n/a
42	POLR2A	chr4:56261530-56263279	ProgFib	skin:	n/a	n/a
43	PML	chr4:56261782-56262392	MCF-7	breast:	n/a	n/a
44	RFX5	chr4:56261217-56262273	Hela-S3	cervix:	n/a	n/a
45	TCF3	chr4:56261854-56262417	GM12878	blood:	n/a	chr4:56262108-56262121
46	RCOR1	chr4:56261457-56262289	Hela-S3	cervix:	n/a	n/a
47	MAX	chr4:56261305-56262333	ECC-1	luminal epithelium:	n/a	chr4:56261670-56261680
48	MAX	chr4:56261226-56263609	NB4	blood:	n/a	chr4:56261670-56261680
49	POLR2A	chr4:56261396-56262912	HepG2	liver:	n/a	n/a
50	CHD2	chr4:56261758-56262848	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:56262105-56262155	ovcar-3	ovarian:	n/a
2	chr4:56262105-56262155	NT2-D1	testis:	n/a
3	chr4:56262105-56262155	HUVEC	blood vessel:	n/a
4	chr4:56262105-56262155	HAEpiC	amniotic membrane:	n/a
5	chr4:56262105-56262155	NH-A	brain:	n/a
6	chr4:56262105-56262155	HepG2	liver:	n/a
7	chr4:56262105-56262155	HPAEpiC	pulmonary alveolar:	n/a
8	chr4:56262105-56262155	Jurkat	blood:	n/a
9	chr4:56262105-56262155	PANC-1	pancreas:	n/a
10	chr4:56262105-56262155	HCM	heart:	n/a
11	chr4:56262105-56262155	K562	blood:	n/a
12	chr4:56262105-56262155	AG10803	skin:	n/a
13	chr4:56262105-56262155	AoSMC	blood vessel:	n/a
14	chr4:56262105-56262155	AG04450	lung:	fetal
15	chr4:56262105-56262155	HCPEpiC	choroid plexus:	n/a
16	chr4:56262105-56262155	HIPEpiC	eye:	n/a
17	chr4:56262105-56262155	HEEpiC	esophagus:	n/a
18	chr4:56262105-56262155	PFSK-1	brain:	n/a
19	chr4:56262105-56262155	A549	lung:	n/a
20	chr4:56262105-56262155	BE2_C	brain:	n/a
21	chr4:56262105-56262155	NB4	blood:	n/a
22	chr4:56262105-56262155	MCF-7	breast:	n/a
23	chr4:56262105-56262155	GM06990	blood:	n/a
24	chr4:56262105-56262155	HL-60	blood:	n/a
25	chr4:56262105-56262155	ProgFib	skin:	n/a
26	chr4:56262105-56262155	T-47D	breast:	n/a
27	chr4:56262105-56262155	GM12878	blood:	n/a
28	chr4:56262105-56262155	HMEC	breast:	n/a
29	chr4:56262105-56262155	HEK293	kidney:	embryo
30	chr4:56262105-56262155	BJ	skin:	n/a
31	chr4:56262105-56262155	MCF10A-Er-Src	breast:	n/a
32	chr4:56262105-56262155	NHDF-neo	bronchial:	n/a
33	chr4:56262105-56262155	AG09309	skin:	n/a
34	chr4:56262105-56262155	HNPCEpiC	eye:	n/a
35	chr4:56262105-56262155	PrEC	prostate:	n/a
36	chr4:56262105-56262155	HRE	kidney:	n/a
37	chr4:56262105-56262155	SAEC	small airway:	n/a
38	chr4:56262105-56262155	CMK	blood:	n/a
39	chr4:56262105-56262155	HCT-116	colon:	n/a
40	chr4:56262105-56262155	SKMC	muscle:	n/a
41	chr4:56262105-56262155	LNCaP	prostate:	n/a
42	chr4:56262105-56262155	SK-N-SH	brain:	n/a
43	chr4:56262105-56262155	HCF	heart:	n/a
44	chr4:56262105-56262155	GM12892	blood:	n/a
45	chr4:56262105-56262155	HRPEpiC	eye:	n/a
46	chr4:56262105-56262155	H1-hESC	embryonic stem cell:	embryo
47	chr4:56262105-56262155	NHBE	bronchial:	n/a
48	chr4:56262105-56262155	Caco-2	colon:	n/a
49	chr4:56262105-56262155	RPTEC	kidney:	n/a
50	chr4:56262105-56262155	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:
2	chr3:150125609..150126516-chr4:56261520..56262416,2	HCT-116	colon:
3	chr4:56222050..56228109-chr4:56258616..56264786,10	MCF-7	breast:
4	chr2:43453212..43454058-chr4:56261845..56262526,2	NB4	blood:
5	chr18:56338349..56338859-chr4:56262021..56262530,2	HCT-116	colon:
6	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
7	chr4:56245537..56248832-chr4:56260791..56264132,6	MCF-7	breast:
8	chr4:56252554..56257772-chr4:56259709..56263846,8	MCF-7	breast:
9	chr4:56211096..56216124-chr4:56256262..56265067,20	K562	blood:
10	chr4:56211242..56218739-chr4:56258356..56267013,28	MCF-7	breast:
11	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
12	chr4:56260988..56264413-chr4:56410743..56414640,3	K562	blood:
13	chr4:56248184..56250642-chr4:56260280..56262635,2	K562	blood:
14	chr19:3985082..3985890-chr4:56261509..56262195,2	Hela-S3	cervix:
15	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:
16	chr4:56245158..56247160-chr4:56262133..56263862,2	K562	blood:
17	chr16:67313002..67313543-chr4:56261724..56262428,2	NB4	blood:

Variant related genes	Relation type
TMEM165	TF binding region
SRD5A3-AS1	TF binding region
TMEM165	CpG island
SRD5A3-AS1	CpG island
ENSG00000134852	Chromatin interaction
ENSG00000167658	Chromatin interaction
ENSG00000273257	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000196155	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000172175	Chromatin interaction
ENSG00000251111	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking 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 lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers 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 lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv3440757	chr4:56261420-56263968	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr4:56261200-56262600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr4:56261200-56263000	Active TSS	Fetal Brain Female	brain
3	chr4:56261200-56263400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:56261200-56263400	Active TSS	Osteobl	bone
5	chr4:56261200-56264800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr4:56261200-56265200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:56261400-56262400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:56261400-56262800	Active TSS	Primary T cells from cord blood	blood
9	chr4:56261400-56262800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr4:56261400-56263000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:56261400-56263000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr4:56261400-56263200	Active TSS	Brain Germinal Matrix	brain
13	chr4:56261400-56263200	Active TSS	Colonic Mucosa	Colon
14	chr4:56261400-56263200	Active TSS	Fetal Stomach	stomach
15	chr4:56261400-56263400	Active TSS	HSMM	muscle
16	chr4:56261400-56263600	Active TSS	Brain Substantia Nigra	brain
17	chr4:56261400-56263800	Active TSS	Fetal Muscle Trunk	muscle
18	chr4:56261400-56264000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:56261400-56264000	Active TSS	Left Ventricle	heart
20	chr4:56261400-56264600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:56261400-56264600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:56261400-56264800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:56261400-56264800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:56261400-56264800	Active TSS	Fetal Kidney	kidney
25	chr4:56261400-56264800	Active TSS	Ovary	ovary
26	chr4:56261400-56264800	Active TSS	Right Ventricle	heart
27	chr4:56261400-56265000	Active TSS	H1 Cell Line	embryonic stem cell
28	chr4:56261400-56265200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:56261400-56265200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:56261400-56265200	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr4:56261400-56265400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:56261400-56265400	Active TSS	H9 Cell Line	embryonic stem cell
33	chr4:56261400-56265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:56261400-56265400	Active TSS	Aorta	Aorta
35	chr4:56261400-56265400	Active TSS	Lung	lung
36	chr4:56261400-56265400	Active TSS	Psoas Muscle	Psoas
37	chr4:56261400-56265600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr4:56261400-56265600	Active TSS	HSMMtube	muscle
39	chr4:56261400-56266000	Active TSS	Right Atrium	heart
40	chr4:56261600-56262200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:56261600-56262200	Weak transcription	Stomach Mucosa	stomach
42	chr4:56261600-56262400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:56261600-56262600	Active TSS	Primary B cells from peripheral blood	blood
44	chr4:56261600-56262600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:56261600-56262800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr4:56261600-56262800	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr4:56261600-56262800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:56261600-56263000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:56261600-56263000	Active TSS	Adipose Nuclei	Adipose
50	chr4:56261600-56263000	Active TSS	Rectal Mucosa Donor 31	rectum

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