Variant report

Variant	rs2296014
Chromosome Location	chr4:20254387-20254388
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	POLR2A	chr4:20254298-20254688	MCF-7	breast:	n/a	n/a
2	ZBTB7A	chr4:20253025-20254617	ECC-1	luminal epithelium:	n/a	chr4:20253322-20253331 chr4:20253750-20253758
3	POLR2A	chr4:20254283-20254749	SK-N-SH	brain:	n/a	n/a
4	TBP	chr4:20254339-20254656	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF263	chr4:20253709-20255153	HEK293-T-REx	kidney:	n/a	n/a
6	POLR2A	chr4:20254355-20254604	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:20254384-20254778	Gliobla	brain:	n/a	n/a
8	MAX	chr4:20254169-20255058	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZKSCAN1	chr4:20254373-20254391	Hela-S3	cervix:	n/a	n/a
10	MAX	chr4:20254234-20254996	SK-N-SH	brain:	n/a	n/a
11	CHD2	chr4:20254101-20254405	Hela-S3	cervix:	n/a	n/a
12	MAX	chr4:20252775-20254559	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
13	POLR2A	chr4:20254383-20254811	ProgFib	skin:	n/a	n/a
14	POLR2A	chr4:20254244-20254755	HUVEC	blood vessel:	n/a	n/a
15	TAF1	chr4:20254280-20254623	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr4:20254233-20254944	PFSK-1	brain:	n/a	n/a
17	E2F6	chr4:20254214-20255299	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAZ	chr4:20253041-20254964	IMR90	lung:	n/a	chr4:20253386-20253396
19	POLR2A	chr4:20253057-20255631	HEK293	kidney:	n/a	n/a
20	CTCF	chr4:20254240-20254390	HVMF	connective:	n/a	n/a
21	TAF1	chr4:20254310-20254678	SK-N-SH	brain:	n/a	n/a
22	MYC	chr4:20254255-20254464	MCF-7	breast:	n/a	n/a
23	SIN3AK20	chr4:20254290-20255001	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr4:20253330-20255237	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr4:20253112-20254794	ECC-1	luminal epithelium:	n/a	n/a
26	REST	chr4:20253052-20254957	H1-neurons	neurons:	n/a	chr4:20253730-20253748 chr4:20254048-20254061 chr4:20254554-20254574
27	SIN3AK20	chr4:20254285-20254832	PFSK-1	brain:	n/a	n/a
28	REST	chr4:20254264-20254707	PFSK-1	brain:	n/a	chr4:20254554-20254574
29	SIN3A	chr4:20252815-20254790	H1-hESC	embryonic stem cell:	n/a	chr4:20254076-20254085 chr4:20254559-20254573
30	SUZ12	chr4:20253936-20257122	NT2-D1	testis:	n/a	n/a
31	E2F6	chr4:20254249-20255300	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAFK	chr4:20254366-20254780	IMR90	lung:	n/a	chr4:20254563-20254578
33	MAX	chr4:20253024-20254671	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
34	POLR2A	chr4:20254146-20254834	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr4:20253916-20255139	H1-neurons	neurons:	n/a	n/a
36	MAX	chr4:20254285-20255096	SK-N-SH	brain:	n/a	n/a
37	MAX	chr4:20254138-20255026	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZBTB7A	chr4:20253893-20254666	ECC-1	luminal epithelium:	n/a	n/a
39	TAF1	chr4:20254363-20254578	PFSK-1	brain:	n/a	n/a
40	CTBP2	chr4:20254251-20256981	H1-hESC	embryonic stem cell:	n/a	n/a
41	SUZ12	chr4:20254238-20256968	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:20253180-20254618	Hela-S3	cervix:	n/a	n/a
43	BACH1	chr4:20254170-20254488	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:20254271-20254680	HUVEC	blood vessel:	n/a	n/a
45	TAF1	chr4:20254317-20254684	PFSK-1	brain:	n/a	n/a
46	MYC	chr4:20254321-20254445	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:20252458..20255013-chr4:20255238..20258452,3	MCF-7	breast:
2	chr4:20252097..20254985-chr4:20256141..20260392,5	MCF-7	breast:
3	chr4:20025908..20028659-chr4:20253195..20254796,2	MCF-7	breast:

Variant related genes	Relation type
SLIT2	TF binding region
ENSG00000145147	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10516347	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516348	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516354	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867613	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867614	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16869447	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869450	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16869454	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869455	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869457	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869461	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869465	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16869475	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869481	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951740	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56967065	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57013929	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61114792	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6832019	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6833323	1.00[EUR][1000 genomes]
rs715214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73803832	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661055	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7668570	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7668724	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7668969	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7668991	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673645	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674173	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878736	chr4:20233035-20279858	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv878737	chr4:20233035-20282334	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3373550	chr4:20252479-20255027	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20252200-20258200	Active TSS	NHDF-Ad	bronchial
2	chr4:20252400-20255200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:20252400-20256400	Active TSS	Brain Anterior Caudate	brain
4	chr4:20252400-20257000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr4:20252400-20257400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:20252600-20254400	Active TSS	Right Atrium	heart
7	chr4:20252600-20255000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:20252600-20255000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr4:20252600-20255000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:20252600-20255600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:20252600-20257000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr4:20252600-20257200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:20252600-20257400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:20252600-20257800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:20252800-20254400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr4:20252800-20254400	Active TSS	Fetal Kidney	kidney
17	chr4:20252800-20254400	Active TSS	Rectal Smooth Muscle	rectum
18	chr4:20252800-20254800	Active TSS	Left Ventricle	heart
19	chr4:20252800-20257000	Active TSS	Osteobl	bone
20	chr4:20252800-20258600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:20253000-20254400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr4:20253000-20254400	Active TSS	Brain Hippocampus Middle	brain
23	chr4:20253000-20254600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:20253000-20254600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr4:20253000-20255200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr4:20253000-20256600	Bivalent/Poised TSS	Thymus	Thymus
27	chr4:20253000-20256800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
28	chr4:20253000-20257000	Active TSS	Hela-S3	cervix
29	chr4:20253000-20257400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:20253000-20257600	Active TSS	Colon Smooth Muscle	Colon
31	chr4:20253000-20258000	Active TSS	Placenta Amnion	Placenta Amnion
32	chr4:20253000-20259000	Active TSS	Aorta	Aorta
33	chr4:20253200-20254800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr4:20253200-20256000	Active TSS	Muscle Satellite Cultured Cells	--
35	chr4:20253200-20256600	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:20253200-20256800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:20253200-20256800	Active TSS	NHLF	lung
38	chr4:20253200-20257000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:20253200-20257000	Active TSS	NHEK	skin
40	chr4:20253200-20257600	Active TSS	Brain Angular Gyrus	brain
41	chr4:20253600-20254400	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr4:20253600-20254600	Flanking Bivalent TSS/Enh	Placenta	Placenta
43	chr4:20253600-20254800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:20253600-20254800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:20253600-20255000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
46	chr4:20253600-20256800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:20253600-20257000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:20253800-20254400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:20253800-20254600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:20253800-20254600	Flanking Active TSS	Liver	Liver

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