Variant report

Variant	rs1623306
Chromosome Location	chr4:57773595-57773596
allele	C/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	SP4	chr4:57773590-57774022	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773953 chr4:57773938-57773954 chr4:57773940-57773956
2	ZNF384	chr4:57773528-57773810	GM12878	blood:	n/a	n/a
3	SP1	chr4:57773313-57773965	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773954 chr4:57773939-57773953 chr4:57773943-57773953 chr4:57773944-57773953 chr4:57773942-57773953 chr4:57773943-57773953 chr4:57773942-57773954 chr4:57773944-57773953 chr4:57773943-57773952
4	CTBP2	chr4:57773280-57774131	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr4:57773562-57773835	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr4:57773486-57773995	K562	blood:	n/a	n/a
7	RCOR1	chr4:57773423-57773620	K562	blood:	n/a	n/a
8	MXI1	chr4:57773345-57776166	IMR90	lung:	n/a	n/a
9	TBP	chr4:57773376-57774951	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:57773482-57774002	SK-N-MC	brain:	n/a	n/a
11	EP300	chr4:57773581-57773945	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr4:57773105-57774259	H1-hESC	embryonic stem cell:	n/a	chr4:57774088-57774097
13	GTF2F1	chr4:57773548-57773806	H1-hESC	embryonic stem cell:	n/a	n/a
14	NANOG	chr4:57773256-57774100	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF143	chr4:57773032-57773971	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr4:57773524-57773876	H1-hESC	embryonic stem cell:	n/a	n/a
17	SP4	chr4:57773550-57774029	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773953 chr4:57773938-57773954 chr4:57773940-57773956
18	MAX	chr4:57773547-57774129	SK-N-SH	brain:	n/a	n/a
19	EP300	chr4:57773508-57774125	H1-hESC	embryonic stem cell:	n/a	chr4:57774097-57774113
20	SP1	chr4:57773236-57774607	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773954 chr4:57773939-57773953 chr4:57773943-57773953 chr4:57773944-57773953 chr4:57773942-57773953 chr4:57773943-57773953 chr4:57773942-57773954 chr4:57773944-57773953 chr4:57773943-57773952 chr4:57774283-57774297
21	NANOG	chr4:57773469-57773947	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr4:57773572-57774062	H1-hESC	embryonic stem cell:	n/a	chr4:57773898-57773908
23	JUND	chr4:57773247-57773956	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr4:57773462-57773979	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3A	chr4:57773045-57776084	H1-hESC	embryonic stem cell:	n/a	chr4:57774969-57774978 chr4:57774574-57774587 chr4:57774972-57774985 chr4:57774938-57774951 chr4:57774480-57774493 chr4:57774388-57774401 chr4:57774851-57774862
26	MXI1	chr4:57773202-57773912	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAZ	chr4:57773290-57775623	K562	blood:	n/a	n/a
28	SIN3AK20	chr4:57773591-57774882	MCF-7	breast:	n/a	n/a
29	POU5F1	chr4:57773491-57773964	H1-hESC	embryonic stem cell:	n/a	n/a
30	SIN3AK20	chr4:57773491-57774081	H1-hESC	embryonic stem cell:	n/a	n/a
31	POU5F1	chr4:57773426-57773936	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr4:57773588-57774085	H1-hESC	embryonic stem cell:	n/a	n/a
33	CREB1	chr4:57773496-57774172	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57772988..57775343-chr4:57776220..57778579,3	MCF-7	breast:
2	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
3	chr4:57302175..57303989-chr4:57773484..57775623,2	MCF-7	breast:
4	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:
5	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:

Variant related genes	Relation type
REST	TF binding region
ENSG00000084092	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10003229	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612191	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1622434	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1718875	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2412760	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2412770	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458552	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605409	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28625367	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106530	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58228066	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839385	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6849007	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs708547	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7667084	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7675979	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs781545	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs781551	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs781553	0.89[AMR][1000 genomes]
rs781554	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs781556	0.82[AMR][1000 genomes]
rs781667	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781670	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv12676	chr4:57772270-57775584	Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv3374947	chr4:57773220-57776168	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3389347	chr4:57773345-57775893	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv594205	chr4:57773442-57775064	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv594206	chr4:57773595-57775543	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57772600-57773600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
2	chr4:57772800-57773600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
3	chr4:57772800-57773800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:57772800-57773800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr4:57772800-57776200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:57773000-57773600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:57773000-57773600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr4:57773000-57773600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:57773000-57773600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr4:57773000-57773600	Flanking Active TSS	Fetal Lung	lung
11	chr4:57773000-57773600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr4:57773000-57773600	Flanking Active TSS	Thymus	Thymus
13	chr4:57773000-57773800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr4:57773000-57773800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr4:57773000-57773800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr4:57773000-57773800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr4:57773000-57773800	Enhancers	Lung	lung
18	chr4:57773000-57773800	Enhancers	Spleen	Spleen
19	chr4:57773000-57774000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr4:57773000-57774800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr4:57773000-57776000	Active TSS	Rectal Smooth Muscle	rectum
22	chr4:57773200-57773600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr4:57773200-57773600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:57773200-57773600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:57773200-57773600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:57773200-57773600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:57773200-57773600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr4:57773200-57773600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:57773200-57773600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr4:57773200-57773600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:57773200-57773600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:57773200-57773600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:57773200-57773600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr4:57773200-57773600	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr4:57773200-57773600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr4:57773200-57773600	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr4:57773200-57773600	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr4:57773200-57773600	Flanking Active TSS	Fetal Kidney	kidney
39	chr4:57773200-57773600	Flanking Active TSS	Placenta	Placenta
40	chr4:57773200-57773600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr4:57773200-57773600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr4:57773200-57773600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr4:57773200-57773600	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr4:57773200-57773600	Enhancers	Hela-S3	cervix
45	chr4:57773200-57773600	Flanking Bivalent TSS/Enh	K562	blood
46	chr4:57773200-57773600	Flanking Bivalent TSS/Enh	NH-A	brain
47	chr4:57773200-57773600	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
48	chr4:57773200-57773800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:57773200-57773800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr4:57773200-57773800	Flanking Active TSS	Primary B cells from cord blood	blood

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