Variant report

Variant	rs28561081
Chromosome Location	chr4:57396755-57396756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57396718-57398141	PBDE	blood:	n/a	n/a
2	POLR2A	chr4:57396716-57397330	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr4:57396447-57397331	K562	blood:	n/a	n/a
4	POLR2A	chr4:57396700-57397017	HUVEC	blood vessel:	n/a	n/a
5	IRF1	chr4:57396625-57397030	K562	blood:	n/a	n/a
6	PML	chr4:57396597-57397423	K562	blood:	n/a	n/a
7	IRF1	chr4:57396443-57397141	K562	blood:	n/a	n/a
8	POLR2A	chr4:57396714-57397072	U87	brain:	n/a	n/a
9	TAF1	chr4:57396593-57397273	ECC-1	luminal epithelium:	n/a	n/a
10	HCFC1	chr4:57396730-57397360	K562	blood:	n/a	n/a
11	MAX	chr4:57396691-57397281	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr4:57396704-57397347	K562	blood:	n/a	n/a
13	ZBTB33	chr4:57396701-57397344	K562	blood:	n/a	n/a
14	E2F6	chr4:57396572-57398211	K562	blood:	n/a	n/a
15	TBP	chr4:57396695-57397121	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr4:57396747-57397029	HUVEC	blood vessel:	n/a	n/a
17	E2F6	chr4:57396754-57397267	A549	lung:	n/a	n/a
18	POLR2A	chr4:57396645-57397093	HEK293	kidney:	n/a	n/a
19	POLR2A	chr4:57396702-57396912	HUVEC	blood vessel:	n/a	n/a
20	MAX	chr4:57396713-57397248	A549	lung:	n/a	n/a
21	BACH1	chr4:57396697-57397216	K562	blood:	n/a	n/a
22	ZBTB33	chr4:57396722-57397336	SK-N-SH	brain:	n/a	n/a
23	TAF1	chr4:57396681-57397009	K562	blood:	n/a	n/a
24	CCNT2	chr4:57396474-57397574	K562	blood:	n/a	chr4:57396498-57396518
25	POLR2A	chr4:57396363-57397572	K562	blood:	n/a	n/a
26	MYC	chr4:57396476-57397491	K562	blood:	n/a	n/a
27	YY1	chr4:57396592-57397042	K562	blood:	n/a	n/a
28	EP300	chr4:57396691-57397042	K562	blood:	n/a	n/a
29	POLR2A	chr4:57396678-57397052	SK-N-SH	brain:	n/a	n/a
30	ZBTB33	chr4:57396733-57397188	A549	lung:	n/a	n/a
31	TBP	chr4:57396341-57397523	K562	blood:	n/a	n/a
32	GATA2	chr4:57396207-57397397	SH-SY5Y	brain:	n/a	chr4:57396301-57396314 chr4:57396498-57396511
33	POLR2A	chr4:57396735-57398212	K562	blood:	n/a	n/a
34	POLR2A	chr4:57396689-57397491	K562	blood:	n/a	n/a
35	POLR2A	chr4:57396631-57397120	MCF-7	breast:	n/a	n/a
36	RCOR1	chr4:57396302-57397241	K562	blood:	n/a	n/a
37	POLR2A	chr4:57396565-57397072	K562	blood:	n/a	n/a
38	POLR2A	chr4:57396715-57396964	HCT-116	colon:	n/a	n/a
39	POLR2A	chr4:57396538-57397074	Gliobla	brain:	n/a	n/a
40	POLR2A	chr4:57396718-57396855	GM12878	blood:	n/a	n/a
41	MAX	chr4:57396703-57397409	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr4:57396725-57396989	MCF10A-Er-Src	breast:	n/a	n/a
43	HEY1	chr4:57396689-57397293	K562	blood:	n/a	n/a
44	POLR2A	chr4:57396686-57397169	K562	blood:	n/a	n/a
45	MAZ	chr4:57396333-57398308	K562	blood:	n/a	n/a
46	MXI1	chr4:57396392-57397342	K562	blood:	n/a	chr4:57396571-57396586
47	POLR2A	chr4:57396661-57397086	K562	blood:	n/a	n/a
48	POLR2A	chr4:57396577-57397084	A549	lung:	n/a	n/a
49	BHLHE40	chr4:57396411-57397382	K562	blood:	n/a	n/a
50	TAF1	chr4:57396704-57397111	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57332142..57335262-chr4:57394352..57398997,8	K562	blood:
2	chr4:57331783..57334990-chr4:57394745..57398997,7	K562	blood:
3	chr4:57299474..57303800-chr4:57395386..57399526,7	K562	blood:
4	chr4:57298757..57303397-chr4:57395270..57398462,7	K562	blood:
5	chr4:57251883..57253946-chr4:57396755..57399062,3	K562	blood:

No data

Variant related genes	Relation type
THEGL	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10013766	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10023933	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13150614	0.81[ASN][1000 genomes]
rs28565512	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4280802	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57688783	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv3447654	chr4:57395445-57397943	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57395800-57397200	Active TSS	Brain Anterior Caudate	brain
2	chr4:57396200-57396800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr4:57396200-57396800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:57396200-57396800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:57396200-57396800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:57396200-57396800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:57396200-57396800	Active TSS	Brain Germinal Matrix	brain
8	chr4:57396200-57396800	Active TSS	Duodenum Mucosa	Duodenum
9	chr4:57396200-57396800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
10	chr4:57396200-57396800	Active TSS	Fetal Stomach	stomach
11	chr4:57396200-57396800	Bivalent/Poised TSS	GM12878-XiMat	blood
12	chr4:57396200-57397000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:57396200-57397000	Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr4:57396200-57397000	Active TSS	Muscle Satellite Cultured Cells	--
15	chr4:57396200-57397000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:57396200-57397000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:57396200-57397000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:57396200-57397000	Active TSS	Brain Hippocampus Middle	brain
19	chr4:57396200-57397000	Active TSS	Colonic Mucosa	Colon
20	chr4:57396200-57397000	Active TSS	Ovary	ovary
21	chr4:57396200-57397000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
22	chr4:57396200-57397000	Active TSS	Right Atrium	heart
23	chr4:57396200-57397000	Active TSS	Right Ventricle	heart
24	chr4:57396200-57397000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
25	chr4:57396200-57397000	Active TSS	NHLF	lung
26	chr4:57396200-57397000	Bivalent/Poised TSS	Osteobl	bone
27	chr4:57396200-57397200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:57396200-57397200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:57396200-57397200	Active TSS	Brain Angular Gyrus	brain
30	chr4:57396200-57397200	Active TSS	Brain Cingulate Gyrus	brain
31	chr4:57396200-57397200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:57396200-57397200	Active TSS	Colon Smooth Muscle	Colon
33	chr4:57396200-57397200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr4:57396200-57397200	Active TSS	Fetal Brain Female	brain
35	chr4:57396200-57397200	Active TSS	Fetal Heart	heart
36	chr4:57396200-57397200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr4:57396200-57397200	Active TSS	Fetal Lung	lung
38	chr4:57396200-57397200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:57396200-57397200	Active TSS	A549	lung
40	chr4:57396200-57397400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr4:57396200-57397400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr4:57396200-57397400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr4:57396200-57397400	Active TSS	Brain Substantia Nigra	brain
44	chr4:57396200-57397400	Active TSS	Psoas Muscle	Psoas
45	chr4:57396200-57397400	Active TSS	NHDF-Ad	bronchial
46	chr4:57396200-57397600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr4:57396200-57397600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:57396200-57397600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr4:57396200-57397600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr4:57396200-57397600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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