Variant report

Variant	rs28477228
Chromosome Location	chr4:124320359-124320360
allele	C/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	CHD1	chr4:124320066-124321113	GM12878	blood:	n/a	n/a
2	CTCF	chr4:124319250-124320947	GM12878	blood:	n/a	chr4:124319836-124319854 chr4:124319818-124319831 chr4:124319842-124319851 chr4:124319838-124319851 chr4:124319841-124319854
3	RELA	chr4:124319306-124321439	GM15510	blood:	n/a	n/a
4	TCF12	chr4:124318258-124320535	ECC-1	luminal epithelium:	n/a	chr4:124319740-124319747 chr4:124318543-124318551 chr4:124318678-124318688
5	POLR2A	chr4:124317591-124321155	HL-60	blood:	n/a	n/a
6	CTBP2	chr4:124318422-124320909	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:124319769-124321046	PFSK-1	brain:	n/a	n/a
8	BHLHE40	chr4:124318394-124321321	GM12878	blood:	n/a	chr4:124319567-124319583 chr4:124319731-124319747 chr4:124319756-124319772 chr4:124319602-124319618
9	MXI1	chr4:124317273-124321457	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr4:124317699-124320893	HEK293	kidney:	n/a	n/a
11	TEAD4	chr4:124320200-124320835	HepG2	liver:	n/a	n/a
12	RELA	chr4:124319823-124320816	GM19099	blood:	n/a	n/a
13	MYC	chr4:124317619-124321435	NB4	blood:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
14	RAD21	chr4:124319150-124320998	H1-hESC	embryonic stem cell:	n/a	chr4:124320215-124320227 chr4:124320059-124320073 chr4:124319838-124319848 chr4:124320684-124320696 chr4:124319837-124319850 chr4:124319842-124319855 chr4:124319836-124319848
15	SP1	chr4:124319973-124320389	A549	lung:	n/a	n/a
16	ZNF263	chr4:124317611-124321479	HEK293-T-REx	kidney:	n/a	chr4:124320581-124320590 chr4:124317910-124317931
17	TCF12	chr4:124320297-124321069	A549	lung:	n/a	n/a
18	POLR2A	chr4:124317516-124324681	PANC-1	pancreas:	n/a	n/a
19	HA-E2F1	chr4:124318427-124320649	MCF-7	breast:	n/a	chr4:124319515-124319524 chr4:124319515-124319527 chr4:124319955-124319964 chr4:124319715-124319724 chr4:124319509-124319518
20	MAX	chr4:124317664-124321158	HepG2	liver:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
21	MAZ	chr4:124317421-124321556	IMR90	lung:	n/a	chr4:124319645-124319655 chr4:124319507-124319517
22	SIN3AK20	chr4:124320063-124321144	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr4:124317618-124321804	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr4:124317752-124321674	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr4:124317765-124321517	MCF10A-Er-Src	breast:	n/a	n/a
26	MAX	chr4:124317610-124321006	A549	lung:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
27	HEY1	chr4:124317612-124321355	HepG2	liver:	n/a	chr4:124319753-124319768 chr4:124319591-124319600 chr4:124319710-124319725 chr4:124319510-124319525
28	POLR2A	chr4:124317742-124320986	NB4	blood:	n/a	n/a
29	MAX	chr4:124317600-124321345	NB4	blood:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
30	POLR2A	chr4:124319424-124321038	HepG2	liver:	n/a	n/a
31	SMC3	chr4:124317473-124321772	SK-N-SH	brain:	n/a	chr4:124319838-124319848 chr4:124319838-124319852
32	E2F4	chr4:124320149-124320688	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr4:124318628-124321100	GM18951	blood:	n/a	n/a
34	MXI1	chr4:124317616-124321844	IMR90	lung:	n/a	n/a
35	POLR2A	chr4:124317528-124321086	PBDE	blood:	n/a	n/a
36	POLR2A	chr4:124319546-124320970	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr4:124319864-124321511	SK-N-SH	brain:	n/a	n/a
38	MAX	chr4:124319934-124321109	SK-N-SH	brain:	n/a	n/a
39	SIN3A	chr4:124317692-124321158	H1-hESC	embryonic stem cell:	n/a	chr4:124319758-124319771
40	POLR2A	chr4:124317710-124320795	H1-hESC	embryonic stem cell:	n/a	n/a
41	TEAD4	chr4:124319855-124320397	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAZ	chr4:124318686-124320796	GM12878	blood:	n/a	chr4:124319645-124319655 chr4:124319507-124319517
43	RAD21	chr4:124320235-124321186	IMR90	lung:	n/a	chr4:124320684-124320696
44	RAD21	chr4:124320009-124321125	SK-N-SH_RA	brain:	n/a	chr4:124320215-124320227 chr4:124320059-124320073 chr4:124320684-124320696
45	POLR2A	chr4:124319064-124320961	GM19099	blood:	n/a	n/a
46	RELA	chr4:124318988-124320764	GM12891	blood:	n/a	n/a
47	POLR2A	chr4:124318410-124321124	GM19193	blood:	n/a	n/a
48	RELA	chr4:124319020-124321399	GM18951	blood:	n/a	n/a
49	MAX	chr4:124319972-124320908	SK-N-SH	brain:	n/a	n/a
50	TCF7L2	chr4:124318328-124320477	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:124317259..124319394-chr4:124319799..124323152,4	MCF-7	breast:

Variant related genes	Relation type
SPRY1	TF binding region
ENSG00000164056	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10518414	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098709	0.91[ASN][1000 genomes]
rs13145927	0.90[ASN][1000 genomes]
rs13150612	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs188513	0.89[ASN][1000 genomes]
rs28514996	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs300555	0.93[ASN][1000 genomes]
rs300572	0.96[ASN][1000 genomes]
rs300573	0.83[ASN][1000 genomes]
rs300574	0.98[ASN][1000 genomes]
rs4833277	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833278	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9992811	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006945	chr4:124206328-124503863	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv537240	chr4:124206328-124503863	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv3442616	chr4:124318327-124320875	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr4:124317000-124322000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:124317200-124323000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:124317400-124320800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:124317400-124320800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:124317400-124321200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:124317400-124321400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:124317400-124321600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr4:124317400-124321800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:124317400-124322000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:124317400-124322200	Active TSS	Adipose Nuclei	Adipose
11	chr4:124317400-124322200	Active TSS	Fetal Kidney	kidney
12	chr4:124317400-124322200	Active TSS	Fetal Lung	lung
13	chr4:124317400-124322400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:124317400-124322400	Active TSS	Brain Anterior Caudate	brain
15	chr4:124317400-124322400	Active TSS	Fetal Intestine Large	intestine
16	chr4:124317400-124322400	Active TSS	Stomach Smooth Muscle	stomach
17	chr4:124317400-124322600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:124317400-124322600	Active TSS	Colon Smooth Muscle	Colon
19	chr4:124317400-124322600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:124317400-124322600	Active TSS	Psoas Muscle	Psoas
21	chr4:124317400-124322800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:124317400-124322800	Active TSS	Aorta	Aorta
23	chr4:124317400-124322800	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr4:124317400-124322800	Active TSS	NHLF	lung
25	chr4:124317400-124323200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:124317400-124327000	Active TSS	Right Atrium	heart
27	chr4:124317600-124320600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr4:124317600-124321000	Active TSS	Hela-S3	cervix
29	chr4:124317600-124321200	Active TSS	Fetal Heart	heart
30	chr4:124317600-124321200	Flanking Bivalent TSS/Enh	Dnd41	blood
31	chr4:124317600-124321400	Active TSS	A549	lung
32	chr4:124317600-124321600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr4:124317600-124321600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr4:124317600-124321600	Active TSS	Brain Angular Gyrus	brain
35	chr4:124317600-124321600	Active TSS	Brain Cingulate Gyrus	brain
36	chr4:124317600-124321600	Active TSS	Colonic Mucosa	Colon
37	chr4:124317600-124321600	Active TSS	HSMM	muscle
38	chr4:124317600-124321800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr4:124317600-124321800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:124317600-124321800	Active TSS	Stomach Mucosa	stomach
41	chr4:124317600-124322000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr4:124317600-124322000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:124317600-124322000	Active TSS	Fetal Thymus	thymus
44	chr4:124317600-124322000	Active TSS	Ovary	ovary
45	chr4:124317600-124322200	Active TSS	NHDF-Ad	bronchial
46	chr4:124317600-124322400	Active TSS	HSMMtube	muscle
47	chr4:124317600-124322600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr4:124317600-124322600	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr4:124317600-124322600	Active TSS	Brain Hippocampus Middle	brain
50	chr4:124317600-124322600	Active TSS	Left Ventricle	heart

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