Variant report

Variant	rs66479458
Chromosome Location	chr4:7941788-7941789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr4:7941323-7941875	H1-hESC	embryonic stem cell:	n/a	n/a
2	NRF1	chr4:7941282-7942050	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr4:7941673-7941876	A549	lung:	n/a	n/a
4	REST	chr4:7941267-7941924	H1-neurons	neurons:	n/a	n/a
5	HDAC2	chr4:7941190-7941893	HepG2	liver:	n/a	n/a
6	CHD1	chr4:7938516-7942221	IMR90	lung:	n/a	n/a
7	POLR2A	chr4:7941661-7941861	A549	lung:	n/a	n/a
8	POLR2A	chr4:7939632-7941984	HUVEC	blood vessel:	n/a	n/a
9	KAP1	chr4:7941770-7941987	HEK293	kidney:	n/a	n/a
10	EGR1	chr4:7941529-7941794	K562	blood:	n/a	n/a
11	POLR2A	chr4:7939500-7942061	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr4:7941359-7941941	HCT-116	colon:	n/a	n/a
13	POLR2A	chr4:7941300-7941839	U87	brain:	n/a	n/a
14	POLR2A	chr4:7941220-7941895	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr4:7941125-7942031	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr4:7941190-7941922	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr4:7941056-7941844	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr4:7940773-7941987	MCF-7	breast:	n/a	n/a
19	CHD2	chr4:7941395-7941935	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:7941216-7942047	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr4:7940441-7942003	HUVEC	blood vessel:	n/a	n/a
22	MAZ	chr4:7941457-7941850	HepG2	liver:	n/a	n/a
23	ZBTB7A	chr4:7941704-7941844	HepG2	liver:	n/a	n/a
24	POLR2A	chr4:7939516-7942080	HUVEC	blood vessel:	n/a	n/a
25	SP4	chr4:7941573-7941918	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF143	chr4:7941766-7941936	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr4:7941192-7941811	Gliobla	brain:	n/a	n/a
28	POLR2A	chr4:7941721-7941897	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr4:7941205-7942079	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr4:7941071-7941984	HUVEC	blood vessel:	n/a	n/a
31	CREB1	chr4:7941438-7941826	A549	lung:	n/a	n/a
32	POLR2A	chr4:7941124-7941945	ProgFib	skin:	n/a	n/a
33	POLR2A	chr4:7941217-7941854	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr4:7940681-7941859	Hela-S3	cervix:	n/a	n/a
35	RCOR1	chr4:7941380-7941971	Hela-S3	cervix:	n/a	n/a
36	MAZ	chr4:7939417-7942102	IMR90	lung:	n/a	chr4:7940793-7940802
37	POLR2A	chr4:7941752-7941892	A549	lung:	n/a	n/a
38	HEY1	chr4:7941373-7941980	HepG2	liver:	n/a	n/a
39	MAZ	chr4:7941056-7941999	Hela-S3	cervix:	n/a	n/a
40	NFYB	chr4:7941631-7941871	K562	blood:	n/a	n/a
41	POLR2A	chr4:7941685-7941941	SK-N-SH	brain:	n/a	n/a
42	CHD2	chr4:7941369-7941800	HepG2	liver:	n/a	n/a
43	POLR2A	chr4:7941158-7942001	HUVEC	blood vessel:	n/a	n/a
44	PAX5	chr4:7941305-7941792	GM12892	blood:	n/a	n/a
45	POLR2A	chr4:7941230-7941973	SK-N-MC	brain:	n/a	n/a
46	SIN3AK20	chr4:7941281-7941841	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr4:7940248-7942132	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr4:7941184-7942061	HepG2	liver:	n/a	n/a
49	ZBTB7A	chr4:7941684-7941806	K562	blood:	n/a	n/a
50	POLR2A	chr4:7940383-7942109	H1-neurons	neurons:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:7941764-7941814	HCPEpiC	choroid plexus:	n/a
2	chr4:7941764-7941814	PrEC	prostate:	n/a
3	chr4:7941764-7941814	HMEC	breast:	n/a
4	chr4:7941764-7941814	HRCEpiC	kidney:	n/a
5	chr4:7941764-7941814	RPTEC	kidney:	n/a
6	chr4:7941764-7941814	AG09319	gingival:	n/a
7	chr4:7941764-7941814	MCF-7	breast:	n/a
8	chr4:7941764-7941814	K562	blood:	n/a
9	chr4:7941764-7941814	HIPEpiC	eye:	n/a
10	chr4:7941764-7941814	HCF	heart:	n/a
11	chr4:7941764-7941814	AG09309	skin:	n/a
12	chr4:7941764-7941814	MCF10A-Er-Src	breast:	n/a
13	chr4:7941764-7941814	CMK	blood:	n/a
14	chr4:7941764-7941814	GM12892	blood:	n/a
15	chr4:7941764-7941814	HNPCEpiC	eye:	n/a
16	chr4:7941764-7941814	ECC-1	luminal epithelium:	n/a
17	chr4:7941764-7941814	AG10803	skin:	n/a
18	chr4:7941764-7941814	AG04449	skin:	fetal
19	chr4:7941764-7941814	HCT-116	colon:	n/a
20	chr4:7941764-7941814	HRPEpiC	eye:	n/a
21	chr4:7941764-7941814	SK-N-SH_RA	brain:	n/a
22	chr4:7941764-7941814	HPAEpiC	pulmonary alveolar:	n/a
23	chr4:7941764-7941814	NT2-D1	testis:	n/a
24	chr4:7941764-7941814	ovcar-3	ovarian:	n/a
25	chr4:7941764-7941814	SK-N-SH	brain:	n/a
26	chr4:7941764-7941814	PANC-1	pancreas:	n/a
27	chr4:7941764-7941814	HepG2	liver:	n/a
28	chr4:7941764-7941814	NB4	blood:	n/a
29	chr4:7941764-7941814	HL-60	blood:	n/a
30	chr4:7941764-7941814	AG04450	lung:	fetal
31	chr4:7941764-7941814	IMR90	lung:	fetal
32	chr4:7941764-7941814	A549	lung:	n/a
33	chr4:7941764-7941814	H1-hESC	embryonic stem cell:	embryo
34	chr4:7941764-7941814	PFSK-1	brain:	n/a
35	chr4:7941764-7941814	GM12878	blood:	n/a
36	chr4:7941764-7941814	HUVEC	blood vessel:	n/a
37	chr4:7941764-7941814	BE2_C	brain:	n/a
38	chr4:7941764-7941814	ProgFib	skin:	n/a
39	chr4:7941764-7941814	Caco-2	colon:	n/a
40	chr4:7941764-7941814	SKMC	muscle:	n/a
41	chr4:7941764-7941814	HCM	heart:	n/a
42	chr4:7941764-7941814	NH-A	brain:	n/a
43	chr4:7941764-7941814	HEK293	kidney:	embryo
44	chr4:7941764-7941814	Hepatocyte	liver:	n/a
45	chr4:7941764-7941814	Jurkat	blood:	n/a
46	chr4:7941764-7941814	SAEC	small airway:	n/a
47	chr4:7941764-7941814	GM06990	blood:	n/a
48	chr4:7941764-7941814	HAEpiC	amniotic membrane:	n/a
49	chr4:7941764-7941814	AoSMC	blood vessel:	n/a
50	chr4:7941764-7941814	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7799366..7802066-chr4:7938906..7941900,2	MCF-7	breast:

No data

Variant related genes	Relation type
AFAP1	TF binding region
AFAP1	CpG island
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12696835	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344223	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2385912	0.84[EUR][1000 genomes]
rs2385914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28446696	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072960	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34740645	0.83[AMR][1000 genomes]
rs58349148	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60272249	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6840305	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846757	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7669433	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7669645	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695142	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695170	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7698368	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9993085	0.88[EUR][1000 genomes];0.87[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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS 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	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3370778	chr4:7940277-7942825	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7937800-7941800	Active TSS	A549	lung
2	chr4:7938200-7941800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:7938800-7941800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:7938800-7941800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:7938800-7941800	Active TSS	NHDF-Ad	bronchial
6	chr4:7939000-7941800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr4:7939200-7941800	Active TSS	Rectal Smooth Muscle	rectum
8	chr4:7939200-7941800	Active TSS	NH-A	brain
9	chr4:7939200-7941800	Active TSS	Osteobl	bone
10	chr4:7939200-7942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:7939400-7941800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:7939400-7941800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:7939400-7942000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr4:7939600-7942000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:7939600-7942000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:7939600-7942000	Active TSS	Aorta	Aorta
17	chr4:7939800-7941800	Active TSS	Esophagus	oesophagus
18	chr4:7939800-7941800	Active TSS	Fetal Kidney	kidney
19	chr4:7939800-7941800	Active TSS	Fetal Stomach	stomach
20	chr4:7939800-7942000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr4:7939800-7942000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr4:7940000-7941800	Active TSS	Placenta Amnion	Placenta Amnion
23	chr4:7940000-7941800	Active TSS	Stomach Smooth Muscle	stomach
24	chr4:7940000-7941800	Active TSS	Hela-S3	cervix
25	chr4:7940000-7941800	Active TSS	HSMMtube	muscle
26	chr4:7940000-7942000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr4:7940000-7942000	Active TSS	Colon Smooth Muscle	Colon
28	chr4:7940000-7942000	Active TSS	Gastric	stomach
29	chr4:7940000-7942000	Active TSS	Ovary	ovary
30	chr4:7940000-7942000	Active TSS	Right Atrium	heart
31	chr4:7940200-7941800	Active TSS	Brain Substantia Nigra	brain
32	chr4:7940200-7941800	Active TSS	Pancreas	Pancrea
33	chr4:7940200-7941800	Active TSS	HSMM	muscle
34	chr4:7940200-7942000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:7940200-7942000	Active TSS	Fetal Intestine Large	intestine
36	chr4:7940200-7942200	Active TSS	Fetal Lung	lung
37	chr4:7940400-7941800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:7940400-7941800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:7940400-7941800	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr4:7940400-7941800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:7940400-7941800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:7940400-7941800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr4:7940400-7941800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr4:7940400-7941800	Active TSS	Brain Anterior Caudate	brain
45	chr4:7940400-7941800	Active TSS	Brain Hippocampus Middle	brain
46	chr4:7940400-7941800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr4:7940400-7941800	Active TSS	Duodenum Mucosa	Duodenum
48	chr4:7940400-7941800	Active TSS	Fetal Intestine Small	intestine
49	chr4:7940400-7941800	Active TSS	Left Ventricle	heart
50	chr4:7940400-7941800	Active TSS	Rectal Mucosa Donor 31	rectum

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