Variant report

Variant	rs560928272
Chromosome Location	chr4:20253568-20253569
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	ZBTB7A	chr4:20253025-20254617	ECC-1	luminal epithelium:	n/a	chr4:20253322-20253331 chr4:20253750-20253758
2	TAF1	chr4:20253060-20254152	ECC-1	luminal epithelium:	n/a	n/a
3	TBP	chr4:20253383-20253610	K562	blood:	n/a	n/a
4	MAX	chr4:20253451-20253764	MCF-7	breast:	n/a	n/a
5	MAX	chr4:20252951-20253935	H1-hESC	embryonic stem cell:	n/a	chr4:20253386-20253396
6	JUND	chr4:20253134-20254055	H1-hESC	embryonic stem cell:	n/a	chr4:20253775-20253789
7	YY1	chr4:20253184-20253836	ECC-1	luminal epithelium:	n/a	chr4:20253572-20253583 chr4:20253365-20253374 chr4:20253571-20253580
8	POLR2A	chr4:20253177-20253884	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr4:20253209-20254030	HUVEC	blood vessel:	n/a	n/a
10	TBP	chr4:20252936-20254055	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr4:20253352-20253866	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr4:20253147-20253891	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr4:20253238-20253898	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr4:20253066-20253887	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr4:20253230-20253873	ProgFib	skin:	n/a	n/a
16	MAX	chr4:20252775-20254559	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
17	EGR1	chr4:20253161-20253708	H1-hESC	embryonic stem cell:	n/a	chr4:20253363-20253376 chr4:20253361-20253371 chr4:20253318-20253331
18	POLR2A	chr4:20253392-20253661	HepG2	liver:	n/a	n/a
19	ZKSCAN1	chr4:20253474-20253595	Hela-S3	cervix:	n/a	n/a
20	MAZ	chr4:20253041-20254964	IMR90	lung:	n/a	chr4:20253386-20253396
21	TAF1	chr4:20253467-20253609	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr4:20253386-20253606	GM12878	blood:	n/a	chr4:20253418-20253425
23	TAF1	chr4:20253407-20253699	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr4:20253393-20253845	U87	brain:	n/a	n/a
25	POLR2A	chr4:20253453-20253634	HepG2	liver:	n/a	n/a
26	POLR2A	chr4:20253057-20255631	HEK293	kidney:	n/a	n/a
27	POLR2A	chr4:20253213-20253825	Gliobla	brain:	n/a	n/a
28	YY1	chr4:20253432-20253778	ECC-1	luminal epithelium:	n/a	chr4:20253572-20253583 chr4:20253571-20253580
29	JUND	chr4:20253450-20253592	H1-hESC	embryonic stem cell:	n/a	n/a
30	E2F6	chr4:20253404-20254076	H1-hESC	embryonic stem cell:	n/a	chr4:20253770-20253779 chr4:20253508-20253517 chr4:20253444-20253453
31	E2F6	chr4:20253470-20253915	A549	lung:	n/a	chr4:20253770-20253779 chr4:20253508-20253517
32	CTCF	chr4:20253540-20253690	HA-sp	spinal cord:	n/a	n/a
33	TAF1	chr4:20253329-20253723	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr4:20253259-20253601	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr4:20253330-20255237	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr4:20253324-20253693	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr4:20253412-20253773	HL-60	blood:	n/a	n/a
38	POLR2A	chr4:20253112-20254794	ECC-1	luminal epithelium:	n/a	n/a
39	MAX	chr4:20252937-20253831	SK-N-SH	brain:	n/a	chr4:20253386-20253396
40	POLR2A	chr4:20253180-20253821	Hela-S3	cervix:	n/a	n/a
41	PBX3	chr4:20253289-20253822	SK-N-SH	brain:	n/a	chr4:20253793-20253813
42	REST	chr4:20253052-20254957	H1-neurons	neurons:	n/a	chr4:20253730-20253748 chr4:20254048-20254061 chr4:20254554-20254574
43	SMC3	chr4:20253245-20254155	Hela-S3	cervix:	n/a	chr4:20253441-20253451 chr4:20254081-20254091
44	TBP	chr4:20253360-20253673	HepG2	liver:	n/a	n/a
45	TCF12	chr4:20253255-20254174	ECC-1	luminal epithelium:	n/a	chr4:20253418-20253425
46	POLR2A	chr4:20253262-20253842	HUVEC	blood vessel:	n/a	n/a
47	SIN3AK20	chr4:20253363-20253717	PFSK-1	brain:	n/a	n/a
48	RAD21	chr4:20253353-20253862	ECC-1	luminal epithelium:	n/a	chr4:20253441-20253451
49	POLR2A	chr4:20253310-20253867	MCF-7	breast:	n/a	n/a
50	NRF1	chr4:20253545-20253698	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:20253556-20253606	GM12892	blood:	n/a
2	chr4:20253556-20253606	GM06990	blood:	n/a
3	chr4:20253556-20253606	HL-60	blood:	n/a
4	chr4:20253556-20253606	K562	blood:	n/a
5	chr4:20253556-20253606	GM12891	blood:	n/a
6	chr4:20253556-20253606	SK-N-SH_RA	brain:	n/a
7	chr4:20253556-20253606	Jurkat	blood:	n/a
8	chr4:20253556-20253606	HepG2	liver:	n/a
9	chr4:20253556-20253606	HMEC	breast:	n/a
10	chr4:20253556-20253606	AG09309	skin:	n/a
11	chr4:20253556-20253606	ProgFib	skin:	n/a
12	chr4:20253556-20253606	AoSMC	blood vessel:	n/a
13	chr4:20253556-20253606	A549	lung:	n/a
14	chr4:20253556-20253606	LNCaP	prostate:	n/a
15	chr4:20253556-20253606	HRPEpiC	eye:	n/a
16	chr4:20253556-20253606	HIPEpiC	eye:	n/a
17	chr4:20253556-20253606	HAEpiC	amniotic membrane:	n/a
18	chr4:20253556-20253606	RPTEC	kidney:	n/a
19	chr4:20253556-20253606	SK-N-MC	brain:	n/a
20	chr4:20253556-20253606	Caco-2	colon:	n/a
21	chr4:20253556-20253606	T-47D	breast:	n/a
22	chr4:20253556-20253606	SK-N-SH	brain:	n/a
23	chr4:20253556-20253606	MCF-7	breast:	n/a
24	chr4:20253556-20253606	SAEC	small airway:	n/a
25	chr4:20253556-20253606	PFSK-1	brain:	n/a
26	chr4:20253556-20253606	U87	brain:	n/a
27	chr4:20253556-20253606	ovcar-3	ovarian:	n/a
28	chr4:20253556-20253606	H1-hESC	embryonic stem cell:	embryo
29	chr4:20253556-20253606	HUVEC	blood vessel:	n/a
30	chr4:20253556-20253606	AG04449	skin:	fetal
31	chr4:20253556-20253606	NHDF-neo	bronchial:	n/a
32	chr4:20253556-20253606	HRCEpiC	kidney:	n/a
33	chr4:20253556-20253606	PANC-1	pancreas:	n/a
34	chr4:20253556-20253606	NHBE	bronchial:	n/a
35	chr4:20253556-20253606	ECC-1	luminal epithelium:	n/a
36	chr4:20253556-20253606	BJ	skin:	n/a
37	chr4:20253556-20253606	HCF	heart:	n/a
38	chr4:20253556-20253606	IMR90	lung:	fetal
39	chr4:20253556-20253606	HNPCEpiC	eye:	n/a
40	chr4:20253556-20253606	AG10803	skin:	n/a
41	chr4:20253556-20253606	NT2-D1	testis:	n/a
42	chr4:20253556-20253606	BE2_C	brain:	n/a
43	chr4:20253556-20253606	HCM	heart:	n/a
44	chr4:20253556-20253606	AG09319	gingival:	n/a
45	chr4:20253556-20253606	GM12878	blood:	n/a
46	chr4:20253556-20253606	HEEpiC	esophagus:	n/a
47	chr4:20253556-20253606	PrEC	prostate:	n/a
48	chr4:20253556-20253606	SKMC	muscle:	n/a
49	chr4:20253556-20253606	HCT-116	colon:	n/a
50	chr4:20253556-20253606	HCPEpiC	choroid plexus:	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
SLIT2	CpG island
ENSG00000145147	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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:105 , 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	chr4:20252600-20254200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:20252600-20254400	Active TSS	Right Atrium	heart
8	chr4:20252600-20255000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr4:20252600-20255000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr4:20252600-20255000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:20252600-20255600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:20252600-20257000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr4:20252600-20257200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:20252600-20257400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:20252600-20257800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:20252800-20253600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:20252800-20253800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:20252800-20253800	Active TSS	Fetal Muscle Leg	muscle
19	chr4:20252800-20253800	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr4:20252800-20253800	Active TSS	HMEC	breast
21	chr4:20252800-20254000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:20252800-20254000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:20252800-20254000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr4:20252800-20254000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
25	chr4:20252800-20254000	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr4:20252800-20254000	Active TSS	Right Ventricle	heart
27	chr4:20252800-20254000	Active TSS	Stomach Smooth Muscle	stomach
28	chr4:20252800-20254200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr4:20252800-20254200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:20252800-20254200	Active TSS	Brain Substantia Nigra	brain
31	chr4:20252800-20254200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
32	chr4:20252800-20254200	Active TSS	Ovary	ovary
33	chr4:20252800-20254400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr4:20252800-20254400	Active TSS	Fetal Kidney	kidney
35	chr4:20252800-20254400	Active TSS	Rectal Smooth Muscle	rectum
36	chr4:20252800-20254800	Active TSS	Left Ventricle	heart
37	chr4:20252800-20257000	Active TSS	Osteobl	bone
38	chr4:20252800-20258600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:20253000-20253600	Bivalent/Poised TSS	Placenta	Placenta
40	chr4:20253000-20253800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:20253000-20253800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:20253000-20253800	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr4:20253000-20253800	Active TSS	Colonic Mucosa	Colon
44	chr4:20253000-20253800	Active TSS	Duodenum Mucosa	Duodenum
45	chr4:20253000-20253800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr4:20253000-20253800	Active TSS	Fetal Stomach	stomach
47	chr4:20253000-20253800	Bivalent/Poised TSS	Fetal Thymus	thymus
48	chr4:20253000-20253800	Active TSS	HepG2	liver
49	chr4:20253000-20254000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:20253000-20254000	Bivalent/Poised TSS	Esophagus	oesophagus

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