Variant report

Variant	rs542606613
Chromosome Location	chr4:87855771-87855772
allele	A/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	TCF12	chr4:87855693-87856666	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr4:87855558-87857751	HUVEC	blood vessel:	n/a	n/a
3	NFIC	chr4:87855325-87856349	GM12878	blood:	n/a	n/a
4	MYC	chr4:87855333-87855973	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr4:87855235-87856363	K562	blood:	n/a	chr4:87856037-87856053 chr4:87855361-87855369
6	TAF1	chr4:87855704-87856450	K562	blood:	n/a	n/a
7	POLR2A	chr4:87855390-87857870	GM12878	blood:	n/a	n/a
8	BRCA1	chr4:87855327-87855947	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr4:87855746-87857756	GM12878	blood:	n/a	n/a
10	CTCF	chr4:87855729-87856553	GM12878	blood:	n/a	chr4:87856038-87856051
11	POLR2A	chr4:87855397-87857921	GM19099	blood:	n/a	n/a
12	ZBTB7A	chr4:87855671-87856089	K562	blood:	n/a	n/a
13	HCFC1	chr4:87855249-87857912	K562	blood:	n/a	n/a
14	IRF1	chr4:87855042-87856705	K562	blood:	n/a	chr4:87856113-87856127 chr4:87856094-87856108 chr4:87855197-87855207 chr4:87856479-87856493
15	ATF2	chr4:87855462-87855977	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:87855719-87856850	GM12891	blood:	n/a	n/a
17	RFX5	chr4:87855389-87856351	GM12878	blood:	n/a	n/a
18	RAD21	chr4:87855635-87856345	Hela-S3	cervix:	n/a	chr4:87856034-87856048
19	ZNF143	chr4:87855714-87856451	GM12878	blood:	n/a	chr4:87856075-87856093
20	EGR1	chr4:87855677-87856377	K562	blood:	n/a	chr4:87856084-87856097 chr4:87856090-87856103 chr4:87856093-87856103 chr4:87856050-87856060 chr4:87856095-87856105
21	ESR1	chr4:87855687-87856020	T-47D	breast:	n/a	chr4:87855914-87855929
22	TAF1	chr4:87855717-87856361	SK-N-SH	brain:	n/a	n/a
23	ZMIZ1	chr4:87855377-87856681	K562	blood:	n/a	n/a
24	POLR2A	chr4:87855314-87857869	NB4	blood:	n/a	n/a
25	BACH1	chr4:87855742-87856572	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:87855525-87857861	GM12892	blood:	n/a	n/a
27	POLR2A	chr4:87855410-87857773	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:87855428-87858463	MCF10A-Er-Src	breast:	n/a	n/a
29	TAF1	chr4:87855686-87856426	A549	lung:	n/a	n/a
30	CTCF	chr4:87855680-87855830	NHDF-neo	bronchial:	n/a	n/a
31	EGR1	chr4:87855719-87856317	K562	blood:	n/a	chr4:87856084-87856097 chr4:87856090-87856103 chr4:87856093-87856103 chr4:87856050-87856060 chr4:87856095-87856105
32	PAX5	chr4:87855759-87856417	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:87855256-87857801	K562	blood:	n/a	n/a
34	NRF1	chr4:87855365-87856728	SK-N-SH	brain:	n/a	chr4:87856095-87856104 chr4:87856050-87856059 chr4:87856179-87856190 chr4:87856191-87856202 chr4:87856210-87856221
35	CEBPD	chr4:87855264-87857762	K562	blood:	n/a	n/a
36	MYC	chr4:87855411-87856395	MCF10A-Er-Src	breast:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
37	MAX	chr4:87855356-87857880	Hela-S3	cervix:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
38	TRIM28	chr4:87855339-87856265	K562	blood:	n/a	n/a
39	RAD21	chr4:87855751-87856533	H1-hESC	embryonic stem cell:	n/a	chr4:87856034-87856048
40	CBX3	chr4:87855592-87856167	K562	blood:	n/a	n/a
41	YY1	chr4:87855764-87856478	HepG2	liver:	n/a	chr4:87856095-87856104 chr4:87856092-87856106
42	MYC	chr4:87855279-87858209	K562	blood:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
43	RELA	chr4:87855422-87856382	GM19099	blood:	n/a	n/a
44	POLR2A	chr4:87855657-87856093	SK-N-MC	brain:	n/a	n/a
45	NR2F2	chr4:87855568-87856688	MCF-7	breast:	n/a	n/a
46	GATA3	chr4:87855656-87856272	MCF-7	breast:	n/a	n/a
47	MAFK	chr4:87855372-87856336	K562	blood:	n/a	chr4:87855387-87855402
48	POLR2A	chr4:87855365-87858037	PBDE	blood:	n/a	n/a
49	CTCF	chr4:87855740-87855890	HCM	heart:	n/a	n/a
50	UBTF	chr4:87855748-87856669	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:87855388..87857616-chr4:87927379..87929131,8	MCF-7	breast:
2	chr4:87854791..87857074-chr4:87968149..87971029,2	K562	blood:
3	chr4:87854638..87857344-chr4:88139505..88141852,2	K562	blood:
4	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
5	chr4:87855268..87857472-chr4:88140405..88143113,3	MCF-7	breast:
6	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
7	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
8	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC10A6-2	chr4:87855639-87856091	NONHSAT097289
2	lnc-SLC10A6-2	chr4:87855639-87856002	NONHSAT097291

Variant related genes	Relation type
C4orf36	TF binding region
AFF1	TF binding region
ENSG00000172493	Chromatin interaction
ENSG00000145332	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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv3421759	chr4:87855153-87857701	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87849800-87855800	Weak transcription	Spleen	Spleen
2	chr4:87854400-87855800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:87854600-87857000	Active TSS	Placenta	Placenta
4	chr4:87854800-87855800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr4:87854800-87855800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:87854800-87855800	Flanking Active TSS	Dnd41	blood
7	chr4:87854800-87856000	Active TSS	Right Atrium	heart
8	chr4:87854800-87856400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:87854800-87857000	Active TSS	K562	blood
10	chr4:87854800-87858600	Active TSS	Right Ventricle	heart
11	chr4:87854800-87859200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr4:87855000-87855800	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr4:87855000-87855800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr4:87855000-87855800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr4:87855000-87855800	Flanking Active TSS	HUVEC	blood vessel
16	chr4:87855000-87856800	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr4:87855000-87857000	Active TSS	Stomach Smooth Muscle	stomach
18	chr4:87855000-87857400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:87855000-87857400	Active TSS	Aorta	Aorta
20	chr4:87855000-87857400	Active TSS	HSMMtube	muscle
21	chr4:87855000-87857800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:87855000-87857800	Active TSS	Brain Angular Gyrus	brain
23	chr4:87855000-87858000	Active TSS	Duodenum Mucosa	Duodenum
24	chr4:87855000-87858000	Active TSS	HMEC	breast
25	chr4:87855000-87858200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr4:87855000-87858400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr4:87855000-87858400	Active TSS	Psoas Muscle	Psoas
28	chr4:87855000-87859000	Active TSS	Colonic Mucosa	Colon
29	chr4:87855000-87859000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr4:87855000-87859800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:87855200-87855800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr4:87855200-87855800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr4:87855200-87855800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:87855200-87855800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr4:87855200-87855800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:87855200-87855800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr4:87855200-87856000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr4:87855200-87856400	Active TSS	Fetal Muscle Trunk	muscle
39	chr4:87855200-87856600	Active TSS	HepG2	liver
40	chr4:87855200-87856800	Active TSS	Primary T cells fromperipheralblood	blood
41	chr4:87855200-87857000	Active TSS	Thymus	Thymus
42	chr4:87855200-87857200	Active TSS	Fetal Intestine Small	intestine
43	chr4:87855200-87857400	Active TSS	Fetal Heart	heart
44	chr4:87855200-87857600	Active TSS	Colon Smooth Muscle	Colon
45	chr4:87855200-87857600	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr4:87855200-87857600	Active TSS	NHDF-Ad	bronchial
47	chr4:87855200-87857800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:87855200-87857800	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr4:87855200-87857800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:87855200-87857800	Active TSS	Brain Inferior Temporal Lobe	brain

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