Variant report

Variant	rs558540025
Chromosome Location	chr4:56261980-56261981
allele	C/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	HDAC2	chr4:56261509-56262138	HepG2	liver:	n/a	chr4:56261622-56261636
6	POLR2A	chr4:56261620-56262356	A549	lung:	n/a	n/a
7	E2F4	chr4:56261555-56262236	MCF10A-Er-Src	breast:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262136-56262146
8	MAX	chr4:56261475-56262910	HepG2	liver:	n/a	chr4:56261670-56261680
9	MYBL2	chr4:56261968-56262460	HepG2	liver:	n/a	n/a
10	POLR2A	chr4:56261418-56262619	PFSK-1	brain:	n/a	n/a
11	MAX	chr4:56261350-56262354	MCF-7	breast:	n/a	chr4:56261670-56261680
12	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
13	E2F4	chr4:56261590-56262783	K562	blood:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262243-56262253 chr4:56262136-56262146 chr4:56262246-56262256
14	POLR2A	chr4:56261604-56262358	HCT-116	colon:	n/a	n/a
15	HEY1	chr4:56261581-56262393	K562	blood:	n/a	chr4:56262325-56262340 chr4:56262103-56262118 chr4:56261904-56261919
16	MXI1	chr4:56260947-56266145	SK-N-SH	brain:	n/a	n/a
17	SIN3AK20	chr4:56261474-56262514	MCF-7	breast:	n/a	n/a
18	RAD21	chr4:56261464-56262288	IMR90	lung:	n/a	n/a
19	POLR2A	chr4:56261568-56262455	HCT-116	colon:	n/a	n/a
20	E2F4	chr4:56261967-56262220	GM12878	blood:	n/a	chr4:56262136-56262146
21	TCF12	chr4:56261960-56262319	GM12878	blood:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
22	POLR2A	chr4:56261482-56262483	U87	brain:	n/a	n/a
23	TCF12	chr4:56261565-56262891	ECC-1	luminal epithelium:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
24	MYC	chr4:56261682-56262133	GM12878	blood:	n/a	n/a
25	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
26	MAFK	chr4:56261479-56262088	K562	blood:	n/a	n/a
27	MAX	chr4:56261385-56262415	A549	lung:	n/a	chr4:56261670-56261680
28	BHLHE40	chr4:56261891-56262345	HepG2	liver:	n/a	n/a
29	POLR2A	chr4:56261662-56262375	HEK293	kidney:	n/a	n/a
30	POLR2A	chr4:56261613-56262500	ECC-1	luminal epithelium:	n/a	n/a
31	NFYB	chr4:56261797-56262231	Hela-S3	cervix:	n/a	chr4:56262046-56262061 chr4:56262046-56262060 chr4:56262043-56262058 chr4:56262046-56262061
32	TBP	chr4:56261474-56262301	GM12878	blood:	n/a	n/a
33	IRF1	chr4:56261495-56262351	K562	blood:	n/a	n/a
34	TAF1	chr4:56261625-56262821	HepG2	liver:	n/a	n/a
35	TAF1	chr4:56261651-56262352	PFSK-1	brain:	n/a	n/a
36	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
37	CREB1	chr4:56261492-56262464	GM12878	blood:	n/a	chr4:56261747-56261760
38	ZEB1	chr4:56261454-56262885	HepG2	liver:	n/a	n/a
39	TAF1	chr4:56261773-56262379	A549	lung:	n/a	n/a
40	MYC	chr4:56261571-56262098	MCF10A-Er-Src	breast:	n/a	chr4:56261670-56261680
41	MAX	chr4:56261507-56262208	A549	lung:	n/a	chr4:56261670-56261680
42	TCF12	chr4:56261674-56262425	A549	lung:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
43	HMGN3	chr4:56261567-56263107	K562	blood:	n/a	n/a
44	POLR2A	chr4:56261530-56263279	ProgFib	skin:	n/a	n/a
45	PML	chr4:56261782-56262392	MCF-7	breast:	n/a	n/a
46	RFX5	chr4:56261217-56262273	Hela-S3	cervix:	n/a	n/a
47	TCF3	chr4:56261854-56262417	GM12878	blood:	n/a	chr4:56262108-56262121
48	RCOR1	chr4:56261457-56262289	Hela-S3	cervix:	n/a	n/a
49	MAX	chr4:56261305-56262333	ECC-1	luminal epithelium:	n/a	chr4:56261670-56261680
50	MAX	chr4:56261226-56263609	NB4	blood:	n/a	chr4:56261670-56261680

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	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
6	chr4:56245537..56248832-chr4:56260791..56264132,6	MCF-7	breast:
7	chr4:56252554..56257772-chr4:56259709..56263846,8	MCF-7	breast:
8	chr4:56211096..56216124-chr4:56256262..56265067,20	K562	blood:
9	chr4:56211242..56218739-chr4:56258356..56267013,28	MCF-7	breast:
10	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
11	chr4:56260988..56264413-chr4:56410743..56414640,3	K562	blood:
12	chr4:56248184..56250642-chr4:56260280..56262635,2	K562	blood:
13	chr19:3985082..3985890-chr4:56261509..56262195,2	Hela-S3	cervix:
14	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:
15	chr16:67313002..67313543-chr4:56261724..56262428,2	NB4	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLOCK-1	chr4:56261962-56262009	ENSG00000249700.4
2	lnc-CLOCK-1	chr4:56261962-56262009	ENSG00000249700.4
3	lnc-CLOCK-1	chr4:56261962-56261997	ENSG00000249700.4
4	lnc-CLOCK-1	chr4:56261962-56262004	ENSG00000249700.4
5	lnc-CLOCK-1	chr4:56261962-56262014	ENSG00000249700.4

Variant related genes	Relation type
TMEM165	TF binding region
ENSG00000152518	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000167658	Chromatin interaction
ENSG00000251111	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000196155	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000273257	Chromatin interaction
ENSG00000134851	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	chr4:56261200-56262000	Active TSS	Fetal Brain Male	brain
2	chr4:56261200-56262600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr4:56261200-56263000	Active TSS	Fetal Brain Female	brain
4	chr4:56261200-56263400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:56261200-56263400	Active TSS	Osteobl	bone
6	chr4:56261200-56264800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:56261200-56265200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:56261400-56262000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:56261400-56262000	Flanking Active TSS	Liver	Liver
10	chr4:56261400-56262000	Active TSS	Fetal Heart	heart
11	chr4:56261400-56262000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr4:56261400-56262400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:56261400-56262800	Active TSS	Primary T cells from cord blood	blood
14	chr4:56261400-56262800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr4:56261400-56263000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:56261400-56263000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr4:56261400-56263200	Active TSS	Brain Germinal Matrix	brain
18	chr4:56261400-56263200	Active TSS	Colonic Mucosa	Colon
19	chr4:56261400-56263200	Active TSS	Fetal Stomach	stomach
20	chr4:56261400-56263400	Active TSS	HSMM	muscle
21	chr4:56261400-56263600	Active TSS	Brain Substantia Nigra	brain
22	chr4:56261400-56263800	Active TSS	Fetal Muscle Trunk	muscle
23	chr4:56261400-56264000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:56261400-56264000	Active TSS	Left Ventricle	heart
25	chr4:56261400-56264600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:56261400-56264600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:56261400-56264800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:56261400-56264800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:56261400-56264800	Active TSS	Fetal Kidney	kidney
30	chr4:56261400-56264800	Active TSS	Ovary	ovary
31	chr4:56261400-56264800	Active TSS	Right Ventricle	heart
32	chr4:56261400-56265000	Active TSS	H1 Cell Line	embryonic stem cell
33	chr4:56261400-56265200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:56261400-56265200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:56261400-56265200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr4:56261400-56265400	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr4:56261400-56265400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr4:56261400-56265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:56261400-56265400	Active TSS	Aorta	Aorta
40	chr4:56261400-56265400	Active TSS	Lung	lung
41	chr4:56261400-56265400	Active TSS	Psoas Muscle	Psoas
42	chr4:56261400-56265600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr4:56261400-56265600	Active TSS	HSMMtube	muscle
44	chr4:56261400-56266000	Active TSS	Right Atrium	heart
45	chr4:56261600-56262200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:56261600-56262200	Weak transcription	Stomach Mucosa	stomach
47	chr4:56261600-56262400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:56261600-56262600	Active TSS	Primary B cells from peripheral blood	blood
49	chr4:56261600-56262600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:56261600-56262800	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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