Variant report

Variant	rs55644945
Chromosome Location	chr4:87856365-87856366
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	CREB1	chr4:87855782-87856461	A549	lung:	n/a	n/a
2	TCF12	chr4:87855693-87856666	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr4:87855558-87857751	HUVEC	blood vessel:	n/a	n/a
4	TCF3	chr4:87855783-87856546	GM12878	blood:	n/a	n/a
5	CTCF	chr4:87856220-87856370	GM12872	blood:	n/a	n/a
6	SPI1	chr4:87855777-87856407	HL-60	blood:	n/a	n/a
7	POLR2A	chr4:87856104-87856449	H1-hESC	embryonic stem cell:	n/a	n/a
8	BHLHE40	chr4:87855861-87856378	HepG2	liver:	n/a	chr4:87856047-87856063
9	TAF1	chr4:87855704-87856450	K562	blood:	n/a	n/a
10	CTCF	chr4:87855851-87856375	GM10266	blood:	n/a	chr4:87856038-87856051
11	POLR2A	chr4:87855390-87857870	GM12878	blood:	n/a	n/a
12	FOS	chr4:87855842-87856605	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr4:87855746-87857756	GM12878	blood:	n/a	n/a
14	CTCF	chr4:87855729-87856553	GM12878	blood:	n/a	chr4:87856038-87856051
15	YY1	chr4:87855806-87856435	K562	blood:	n/a	chr4:87856095-87856104 chr4:87856092-87856106
16	POLR2A	chr4:87855397-87857921	GM19099	blood:	n/a	n/a
17	TCF7L2	chr4:87856233-87857994	Hela-S3	cervix:	n/a	chr4:87857812-87857826 chr4:87857815-87857824 chr4:87857424-87857433
18	STAT3	chr4:87856317-87856673	MCF10A-Er-Src	breast:	n/a	chr4:87856461-87856472 chr4:87856499-87856510
19	CTCF	chr4:87855858-87856406	GM12892	blood:	n/a	chr4:87856038-87856051
20	MAFK	chr4:87855780-87856588	Hela-S3	cervix:	n/a	chr4:87856510-87856519
21	POLR2A	chr4:87855795-87857474	MCF-7	breast:	n/a	n/a
22	HCFC1	chr4:87855249-87857912	K562	blood:	n/a	n/a
23	CTCF	chr4:87856240-87856390	Hela-S3	cervix:	n/a	n/a
24	IRF1	chr4:87855042-87856705	K562	blood:	n/a	chr4:87856113-87856127 chr4:87856094-87856108 chr4:87855197-87855207 chr4:87856479-87856493
25	POLR2A	chr4:87855719-87856850	GM12891	blood:	n/a	n/a
26	ZNF143	chr4:87855714-87856451	GM12878	blood:	n/a	chr4:87856075-87856093
27	CTCF	chr4:87855877-87856527	K562	blood:	n/a	chr4:87856038-87856051
28	EGR1	chr4:87855677-87856377	K562	blood:	n/a	chr4:87856084-87856097 chr4:87856090-87856103 chr4:87856093-87856103 chr4:87856050-87856060 chr4:87856095-87856105
29	CTCF	chr4:87856240-87856390	SK-N-SH_RA	brain:	n/a	n/a
30	CTCF	chr4:87856240-87856390	HCFaa	heart:	n/a	n/a
31	ELF1	chr4:87855790-87856390	K562	blood:	n/a	n/a
32	ZMIZ1	chr4:87855377-87856681	K562	blood:	n/a	n/a
33	POLR2A	chr4:87855314-87857869	NB4	blood:	n/a	n/a
34	CTCF	chr4:87856184-87856384	K562	blood:	n/a	n/a
35	CTCF	chr4:87855902-87856383	MCF-7	breast:	n/a	chr4:87856038-87856051
36	CTCF	chr4:87856220-87856370	SK-N-SH_RA	brain:	n/a	n/a
37	POLR2A	chr4:87856064-87857845	HepG2	liver:	n/a	n/a
38	RAD21	chr4:87855819-87856448	HepG2	liver:	n/a	chr4:87856034-87856048
39	BACH1	chr4:87855742-87856572	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr4:87855525-87857861	GM12892	blood:	n/a	n/a
41	POLR2A	chr4:87855410-87857773	GM12878	blood:	n/a	n/a
42	ELK1	chr4:87855866-87856367	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr4:87855428-87858463	MCF10A-Er-Src	breast:	n/a	n/a
44	TAF1	chr4:87855686-87856426	A549	lung:	n/a	n/a
45	RFX5	chr4:87855889-87856616	HepG2	liver:	n/a	n/a
46	CTCFL	chr4:87856112-87856365	K562	blood:	n/a	n/a
47	PAX5	chr4:87855759-87856417	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:87855256-87857801	K562	blood:	n/a	n/a
49	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
50	CEBPD	chr4:87855264-87857762	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	chr4:87855810..87856702-chr8:142011115..142011980,2	Hela-S3	cervix:
3	chr19:50370328..50370862-chr4:87855882..87856437,2	Hela-S3	cervix:
4	chr17:7387417..7387950-chr4:87855939..87856445,2	Hela-S3	cervix:
5	chr4:87854791..87857074-chr4:87968149..87971029,2	K562	blood:
6	chr4:87855884..87856686-chr6:32939572..32940072,2	HCT-116	colon:
7	chr11:62608643..62609622-chr4:87855968..87856688,2	Hela-S3	cervix:
8	chr4:87854638..87857344-chr4:88139505..88141852,2	K562	blood:
9	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
10	chr4:87855268..87857472-chr4:88140405..88143113,3	MCF-7	breast:
11	chr4:87855994..87856653-chr9:98638123..98638697,2	Hela-S3	cervix:
12	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
13	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
14	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:

Variant related genes	Relation type
C4orf36	TF binding region
AFF1	TF binding region
ENSG00000181222	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000169398	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000039650	Chromatin interaction
ENSG00000172493	Chromatin interaction
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13435377	1.00[AMR][1000 genomes]
rs28585548	1.00[AMR][1000 genomes]
rs28702596	1.00[AMR][1000 genomes]
rs58252316	1.00[AMR][1000 genomes]
rs60111562	1.00[AMR][1000 genomes]
rs60354679	1.00[AMR][1000 genomes]
rs6853105	1.00[AMR][1000 genomes]
rs73837055	1.00[AMR][1000 genomes]
rs73837061	1.00[AMR][1000 genomes]
rs73837062	1.00[AMR][1000 genomes]
rs73837570	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73837572	1.00[AMR][1000 genomes]
rs73837573	1.00[AMR][1000 genomes]
rs73838344	1.00[AMR][1000 genomes]
rs73838352	1.00[AMR][1000 genomes]

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	chr4:87854600-87857000	Active TSS	Placenta	Placenta
2	chr4:87854800-87856400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:87854800-87857000	Active TSS	K562	blood
4	chr4:87854800-87858600	Active TSS	Right Ventricle	heart
5	chr4:87854800-87859200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:87855000-87856800	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr4:87855000-87857000	Active TSS	Stomach Smooth Muscle	stomach
8	chr4:87855000-87857400	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr4:87855000-87857400	Active TSS	Aorta	Aorta
10	chr4:87855000-87857400	Active TSS	HSMMtube	muscle
11	chr4:87855000-87857800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:87855000-87857800	Active TSS	Brain Angular Gyrus	brain
13	chr4:87855000-87858000	Active TSS	Duodenum Mucosa	Duodenum
14	chr4:87855000-87858000	Active TSS	HMEC	breast
15	chr4:87855000-87858200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr4:87855000-87858400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:87855000-87858400	Active TSS	Psoas Muscle	Psoas
18	chr4:87855000-87859000	Active TSS	Colonic Mucosa	Colon
19	chr4:87855000-87859000	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr4:87855000-87859800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:87855200-87856400	Active TSS	Fetal Muscle Trunk	muscle
22	chr4:87855200-87856600	Active TSS	HepG2	liver
23	chr4:87855200-87856800	Active TSS	Primary T cells fromperipheralblood	blood
24	chr4:87855200-87857000	Active TSS	Thymus	Thymus
25	chr4:87855200-87857200	Active TSS	Fetal Intestine Small	intestine
26	chr4:87855200-87857400	Active TSS	Fetal Heart	heart
27	chr4:87855200-87857600	Active TSS	Colon Smooth Muscle	Colon
28	chr4:87855200-87857600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr4:87855200-87857600	Active TSS	NHDF-Ad	bronchial
30	chr4:87855200-87857800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:87855200-87857800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr4:87855200-87857800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:87855200-87857800	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr4:87855200-87857800	Active TSS	Left Ventricle	heart
35	chr4:87855200-87857800	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr4:87855200-87858200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:87855200-87858200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:87855200-87858200	Active TSS	Brain Hippocampus Middle	brain
39	chr4:87855200-87858200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:87855200-87858200	Active TSS	A549	lung
41	chr4:87855200-87858400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:87855200-87858400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr4:87855200-87858600	Active TSS	Stomach Mucosa	stomach
44	chr4:87855200-87859000	Active TSS	Fetal Intestine Large	intestine
45	chr4:87855200-87859200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr4:87855200-87859200	Active TSS	H1 Cell Line	embryonic stem cell
47	chr4:87855200-87859800	Active TSS	GM12878-XiMat	blood
48	chr4:87855200-87859800	Active TSS	Hela-S3	cervix
49	chr4:87855400-87856600	Active TSS	Brain Germinal Matrix	brain
50	chr4:87855400-87856600	Active TSS	Fetal Brain Female	brain

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