Variant report

Variant	rs539310683
Chromosome Location	chr4:56262528-56262529
allele	G/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	GABPA	chr4:56261937-56262696	H1-hESC	embryonic stem cell:	n/a	chr4:56262067-56262076
2	POLR2A	chr4:56262450-56262887	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF7L2	chr4:56262453-56262912	Hela-S3	cervix:	n/a	chr4:56262629-56262636
4	MAX	chr4:56261475-56262910	HepG2	liver:	n/a	chr4:56261670-56261680
5	POLR2A	chr4:56261418-56262619	PFSK-1	brain:	n/a	n/a
6	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
7	E2F4	chr4:56261590-56262783	K562	blood:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262243-56262253 chr4:56262136-56262146 chr4:56262246-56262256
8	MXI1	chr4:56260947-56266145	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr4:56261565-56262891	ECC-1	luminal epithelium:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
10	STAT5A	chr4:56262509-56263119	GM12878	blood:	n/a	chr4:56262758-56262770 chr4:56262752-56262764
11	TAF1	chr4:56261625-56262821	HepG2	liver:	n/a	n/a
12	ZBTB7A	chr4:56262508-56262772	K562	blood:	n/a	n/a
13	ZEB1	chr4:56261454-56262885	HepG2	liver:	n/a	n/a
14	HMGN3	chr4:56261567-56263107	K562	blood:	n/a	n/a
15	POLR2A	chr4:56261530-56263279	ProgFib	skin:	n/a	n/a
16	MAX	chr4:56261226-56263609	NB4	blood:	n/a	chr4:56261670-56261680
17	POLR2A	chr4:56261396-56262912	HepG2	liver:	n/a	n/a
18	CHD2	chr4:56261758-56262848	K562	blood:	n/a	n/a
19	POLR2A	chr4:56261529-56263721	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr4:56261539-56262979	GM15510	blood:	n/a	n/a
21	SPI1	chr4:56261533-56262534	HL-60	blood:	n/a	chr4:56262311-56262324 chr4:56262313-56262322 chr4:56261935-56261942 chr4:56262314-56262321
22	POLR2A	chr4:56261413-56262753	HL-60	blood:	n/a	n/a
23	ZNF143	chr4:56262521-56262584	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr4:56261640-56262892	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:56261562-56262897	K562	blood:	n/a	n/a
26	MAX	chr4:56261394-56262748	HepG2	liver:	n/a	chr4:56261670-56261680
27	TCF7L2	chr4:56261714-56262866	HCT-116	colon:	n/a	chr4:56262629-56262636
28	ZEB1	chr4:56261589-56262557	GM12878	blood:	n/a	n/a
29	TCF7L2	chr4:56261655-56262833	PANC-1	pancreas:	n/a	chr4:56262629-56262636
30	HA-E2F1	chr4:56261378-56263041	MCF-7	breast:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262243-56262253 chr4:56262136-56262146 chr4:56262246-56262256
31	POLR2A	chr4:56261574-56262938	Hela-S3	cervix:	n/a	n/a
32	MYC	chr4:56261270-56263292	K562	blood:	n/a	chr4:56261670-56261680
33	SMARCB1	chr4:56261564-56262860	Hela-S3	cervix:	n/a	n/a
34	MYC	chr4:56261346-56263231	NB4	blood:	n/a	chr4:56261670-56261680
35	TBP	chr4:56261580-56263197	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr4:56261557-56262550	SK-N-SH	brain:	n/a	n/a
37	MXI1	chr4:56261553-56262807	HepG2	liver:	n/a	n/a
38	ELF1	chr4:56261599-56262872	GM12878	blood:	n/a	chr4:56262313-56262324 chr4:56262248-56262257 chr4:56261905-56261917 chr4:56262245-56262254 chr4:56262243-56262255 chr4:56262674-56262686 chr4:56262158-56262170 chr4:56262649-56262661
39	POLR2A	chr4:56261632-56262772	HUVEC	blood vessel:	n/a	n/a
40	MYC	chr4:56261301-56262718	K562	blood:	n/a	chr4:56261670-56261680
41	CHD2	chr4:56261732-56262695	HepG2	liver:	n/a	n/a
42	YY1	chr4:56261376-56262691	GM12878	blood:	n/a	chr4:56262663-56262674 chr4:56262248-56262257 chr4:56261529-56261551 chr4:56262166-56262177 chr4:56262243-56262254 chr4:56261904-56261918 chr4:56262246-56262257 chr4:56262245-56262254
43	TCF7L2	chr4:56262251-56262788	HEK293	kidney:	n/a	chr4:56262629-56262636
44	ETS1	chr4:56261549-56262586	K562	blood:	n/a	chr4:56262313-56262320 chr4:56262307-56262321 chr4:56262246-56262257 chr4:56262243-56262254
45	MAX	chr4:56261266-56263287	HCT-116	colon:	n/a	chr4:56261670-56261680
46	PAX5	chr4:56261772-56262770	GM12892	blood:	n/a	chr4:56262312-56262321
47	CHD2	chr4:56261487-56263292	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr4:56261586-56262917	GM12878	blood:	n/a	n/a
49	POLR2A	chr4:56261480-56263519	GM18505	blood:	n/a	n/a
50	POLR2A	chr4:56261304-56265017	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:
2	chr4:56262170..56264152-chr4:56264363..56265916,3	K562	blood:
3	chr4:56222050..56228109-chr4:56258616..56264786,10	MCF-7	breast:
4	chr18:56338349..56338859-chr4:56262021..56262530,2	HCT-116	colon:
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	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:
14	chr4:56245158..56247160-chr4:56262133..56263862,2	K562	blood:

Variant related genes	Relation type
SRD5A3-AS1	TF binding region
TMEM165	TF binding region
ENSG00000172175	Chromatin interaction
ENSG00000273257	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000251111	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	chr4:56261400-56262800	Active TSS	Primary T cells from cord blood	blood
8	chr4:56261400-56262800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr4:56261400-56263000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:56261400-56263000	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr4:56261400-56263200	Active TSS	Brain Germinal Matrix	brain
12	chr4:56261400-56263200	Active TSS	Colonic Mucosa	Colon
13	chr4:56261400-56263200	Active TSS	Fetal Stomach	stomach
14	chr4:56261400-56263400	Active TSS	HSMM	muscle
15	chr4:56261400-56263600	Active TSS	Brain Substantia Nigra	brain
16	chr4:56261400-56263800	Active TSS	Fetal Muscle Trunk	muscle
17	chr4:56261400-56264000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:56261400-56264000	Active TSS	Left Ventricle	heart
19	chr4:56261400-56264600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:56261400-56264600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:56261400-56264800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:56261400-56264800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:56261400-56264800	Active TSS	Fetal Kidney	kidney
24	chr4:56261400-56264800	Active TSS	Ovary	ovary
25	chr4:56261400-56264800	Active TSS	Right Ventricle	heart
26	chr4:56261400-56265000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr4:56261400-56265200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:56261400-56265200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:56261400-56265200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr4:56261400-56265400	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr4:56261400-56265400	Active TSS	H9 Cell Line	embryonic stem cell
32	chr4:56261400-56265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:56261400-56265400	Active TSS	Aorta	Aorta
34	chr4:56261400-56265400	Active TSS	Lung	lung
35	chr4:56261400-56265400	Active TSS	Psoas Muscle	Psoas
36	chr4:56261400-56265600	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr4:56261400-56265600	Active TSS	HSMMtube	muscle
38	chr4:56261400-56266000	Active TSS	Right Atrium	heart
39	chr4:56261600-56262600	Active TSS	Primary B cells from peripheral blood	blood
40	chr4:56261600-56262600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:56261600-56262800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr4:56261600-56262800	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr4:56261600-56262800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:56261600-56263000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:56261600-56263000	Active TSS	Adipose Nuclei	Adipose
46	chr4:56261600-56263000	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr4:56261600-56263200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:56261600-56263200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:56261600-56263200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:56261600-56263200	Active TSS	Primary monocytes fromperipheralblood	blood

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