Variant report

Variant	rs56721576
Chromosome Location	chr4:130015087-130015088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:159)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:159 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:130014275-130015087	Gliobla	brain:	n/a	n/a
2	MXI1	chr4:130012946-130016268	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr4:130014165-130015091	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:130013816-130015128	GM19099	blood:	n/a	n/a
5	SIN3A	chr4:130014099-130015151	GM12878	blood:	n/a	chr4:130014674-130014687
6	POLR2A	chr4:130014245-130015106	NB4	blood:	n/a	n/a
7	POLR2A	chr4:130014164-130015109	MCF10A-Er-Src	breast:	n/a	n/a
8	RCOR1	chr4:130013827-130015269	K562	blood:	n/a	n/a
9	FOXM1	chr4:130014122-130015272	ECC-1	luminal epithelium:	n/a	n/a
10	RCOR1	chr4:130013701-130015157	Hela-S3	cervix:	n/a	n/a
11	NFYB	chr4:130014560-130015280	K562	blood:	n/a	n/a
12	MAX	chr4:130014170-130015120	MCF-7	breast:	n/a	n/a
13	FOXM1	chr4:130014014-130015358	ECC-1	luminal epithelium:	n/a	n/a
14	SMC3	chr4:130014610-130015087	HepG2	liver:	n/a	n/a
15	EBF1	chr4:130013910-130015276	GM12878	blood:	n/a	n/a
16	TAF1	chr4:130014147-130015107	ECC-1	luminal epithelium:	n/a	n/a
17	GTF2F1	chr4:130014375-130015257	Hela-S3	cervix:	n/a	n/a
18	FOXM1	chr4:130014002-130015194	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:130014079-130015126	GM19193	blood:	n/a	n/a
20	STAT1	chr4:130014266-130015169	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:130011739-130015326	IMR90	lung:	n/a	n/a
22	TBL1XR1	chr4:130014386-130015499	K562	blood:	n/a	n/a
23	TBP	chr4:130013168-130015332	Hela-S3	cervix:	n/a	n/a
24	BRCA1	chr4:130013927-130015098	Hela-S3	cervix:	n/a	n/a
25	CREB1	chr4:130014425-130015128	ECC-1	luminal epithelium:	n/a	n/a
26	CHD2	chr4:130014180-130015185	GM12878	blood:	n/a	n/a
27	FOXM1	chr4:130014175-130015088	GM12878	blood:	n/a	n/a
28	CEBPB	chr4:130014365-130015113	HCT-116	colon:	n/a	n/a
29	POLR2A	chr4:130014203-130015123	U87	brain:	n/a	n/a
30	TAF1	chr4:130014237-130015181	H1-neurons	neurons:	n/a	n/a
31	WRNIP1	chr4:130013887-130015198	GM12878	blood:	n/a	n/a
32	TBP	chr4:130013915-130015266	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:130013815-130015194	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:130013932-130015123	GM18505	blood:	n/a	n/a
35	MAX	chr4:130014017-130015160	ECC-1	luminal epithelium:	n/a	n/a
36	CHD2	chr4:130014277-130015112	HepG2	liver:	n/a	n/a
37	POLR2A	chr4:130013800-130015307	GM12878	blood:	n/a	n/a
38	POLR2A	chr4:130012893-130015801	MCF10A-Er-Src	breast:	n/a	n/a
39	MXI1	chr4:130013134-130015186	GM12878	blood:	n/a	n/a
40	MAX	chr4:130014124-130015161	HepG2	liver:	n/a	n/a
41	RUNX3	chr4:130014214-130015267	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:130014096-130015111	HL-60	blood:	n/a	n/a
43	MAX	chr4:130014166-130015102	A549	lung:	n/a	n/a
44	JUND	chr4:130014016-130015564	K562	blood:	n/a	n/a
45	ATF2	chr4:130014395-130015120	GM12878	blood:	n/a	chr4:130014748-130014762
46	SIN3AK20	chr4:130014146-130015097	SK-N-SH	brain:	n/a	n/a
47	BCLAF1	chr4:130014041-130015090	GM12878	blood:	n/a	chr4:130014626-130014639 chr4:130014891-130014900 chr4:130014631-130014640
48	POLR2A	chr4:130014111-130015192	GM12878	blood:	n/a	n/a
49	JUND	chr4:130013834-130015304	SK-N-SH	brain:	n/a	n/a
50	UBTF	chr4:130013763-130015245	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:130015087-130015137	SK-N-SH	brain:	n/a
2	chr4:130015087-130015137	CMK	blood:	n/a
3	chr4:130015087-130015137	PANC-1	pancreas:	n/a
4	chr4:130015087-130015137	NHDF-neo	bronchial:	n/a
5	chr4:130015087-130015137	SK-N-SH_RA	brain:	n/a
6	chr4:130015087-130015137	SAEC	small airway:	n/a
7	chr4:130015087-130015137	SKMC	muscle:	n/a
8	chr4:130015087-130015137	AG04450	lung:	fetal
9	chr4:130015087-130015137	HCF	heart:	n/a
10	chr4:130015087-130015137	HNPCEpiC	eye:	n/a
11	chr4:130015087-130015137	K562	blood:	n/a
12	chr4:130015087-130015137	AoSMC	blood vessel:	n/a
13	chr4:130015087-130015137	PrEC	prostate:	n/a
14	chr4:130015087-130015137	AG09309	skin:	n/a
15	chr4:130015087-130015137	GM19239	blood:	n/a
16	chr4:130015087-130015137	HEK293	kidney:	embryo
17	chr4:130015087-130015137	MCF10A-Er-Src	breast:	n/a
18	chr4:130015087-130015137	HL-60	blood:	n/a
19	chr4:130015087-130015137	HMEC	breast:	n/a
20	chr4:130015087-130015137	NT2-D1	testis:	n/a
21	chr4:130015087-130015137	SK-N-MC	brain:	n/a
22	chr4:130015087-130015137	HRE	kidney:	n/a
23	chr4:130015087-130015137	RPTEC	kidney:	n/a
24	chr4:130015087-130015137	HAEpiC	amniotic membrane:	n/a
25	chr4:130015087-130015137	IMR90	lung:	fetal
26	chr4:130015087-130015137	GM12891	blood:	n/a
27	chr4:130015087-130015137	Hepatocyte	liver:	n/a
28	chr4:130015087-130015137	Hela-S3	cervix:	n/a
29	chr4:130015087-130015137	HIPEpiC	eye:	n/a
30	chr4:130015087-130015137	GM12892	blood:	n/a
31	chr4:130015087-130015137	NHBE	bronchial:	n/a
32	chr4:130015087-130015137	A549	lung:	n/a
33	chr4:130015087-130015137	HUVEC	blood vessel:	n/a
34	chr4:130015087-130015137	AG04449	skin:	fetal
35	chr4:130015087-130015137	ECC-1	luminal epithelium:	n/a
36	chr4:130015087-130015137	GM12878	blood:	n/a
37	chr4:130015087-130015137	HepG2	liver:	n/a
38	chr4:130015087-130015137	U87	brain:	n/a
39	chr4:130015087-130015137	H1-hESC	embryonic stem cell:	embryo
40	chr4:130015087-130015137	AG09319	gingival:	n/a
41	chr4:130015087-130015137	HCT-116	colon:	n/a
42	chr4:130015087-130015137	GM06990	blood:	n/a
43	chr4:130015087-130015137	HPAEpiC	pulmonary alveolar:	n/a
44	chr4:130015087-130015137	ovcar-3	ovarian:	n/a
45	chr4:130015087-130015137	BE2_C	brain:	n/a
46	chr4:130015087-130015137	NB4	blood:	n/a
47	chr4:130015087-130015137	HCM	heart:	n/a
48	chr4:130015087-130015137	Caco-2	colon:	n/a
49	chr4:130015087-130015137	MCF-7	breast:	n/a
50	chr4:130015087-130015137	HRPEpiC	eye:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:128703531..128705249-chr4:130014655..130017577,2	K562	blood:
2	chr4:129731090..129733904-chr4:130015000..130016574,3	K562	blood:
3	chr4:130012621..130015537-chr4:130015842..130017627,2	K562	blood:
4	chr4:129730340..129733748-chr4:130013373..130016609,5	K562	blood:

No data

Variant related genes	Relation type
C4orf33	TF binding region
SCLT1	TF binding region
C4orf33	CpG island
SCLT1	CpG island
ENSG00000077684	Chromatin interaction
ENSG00000151470	Chromatin interaction
ENSG00000164070	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs55707740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55714747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55764329	0.91[AFR][1000 genomes]
rs55955516	1.00[AFR][1000 genomes]
rs56002856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56069250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57056827	1.00[AMR][1000 genomes]
rs57243721	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57542268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58053026	0.91[AFR][1000 genomes]
rs58701517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58799593	1.00[AMR][1000 genomes]
rs60005322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60227965	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61267810	1.00[AFR][1000 genomes]
rs61700015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847304	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847305	1.00[AFR][1000 genomes]
rs73847307	0.83[AFR][1000 genomes]
rs73847310	0.91[AFR][1000 genomes]
rs73847312	1.00[AMR][1000 genomes]
rs73847313	1.00[AMR][1000 genomes]
rs73847314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847356	0.91[AFR][1000 genomes]
rs73847358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847383	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847391	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847395	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847398	0.83[AFR][1000 genomes]
rs73847399	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73848906	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73848910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73848913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73848934	1.00[AFR][1000 genomes]
rs73850027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73850028	1.00[AMR][1000 genomes]
rs73850035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73850039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73850041	1.00[AMR][1000 genomes]
rs73850059	1.00[AMR][1000 genomes]
rs73850061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73850062	0.91[AFR][1000 genomes]
rs73850063	0.91[AFR][1000 genomes]
rs73850064	0.91[AFR][1000 genomes];1.00[AMR][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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130011200-130016000	Active TSS	NHLF	lung
2	chr4:130011200-130016400	Active TSS	GM12878-XiMat	blood
3	chr4:130012200-130015400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:130012200-130015400	Active TSS	A549	lung
5	chr4:130012400-130015800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:130012600-130015800	Active TSS	Brain Hippocampus Middle	brain
7	chr4:130012800-130015400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:130012800-130015400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:130012800-130015400	Active TSS	Fetal Muscle Trunk	muscle
10	chr4:130012800-130015400	Active TSS	HMEC	breast
11	chr4:130012800-130015600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:130012800-130018600	Active TSS	K562	blood
13	chr4:130013000-130015200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr4:130013000-130015200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr4:130013000-130015400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:130013000-130015400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:130013000-130015400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:130013000-130015400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr4:130013200-130015200	Active TSS	Esophagus	oesophagus
20	chr4:130013200-130015200	Active TSS	Fetal Kidney	kidney
21	chr4:130013200-130015400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr4:130013200-130015400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr4:130013200-130015400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:130013200-130015400	Active TSS	Aorta	Aorta
25	chr4:130013200-130015400	Active TSS	Brain Cingulate Gyrus	brain
26	chr4:130013200-130015400	Active TSS	Colon Smooth Muscle	Colon
27	chr4:130013200-130015400	Active TSS	Fetal Stomach	stomach
28	chr4:130013200-130015600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr4:130013400-130015200	Active TSS	H1 Cell Line	embryonic stem cell
30	chr4:130013400-130015200	Active TSS	Placenta	Placenta
31	chr4:130013400-130015200	Active TSS	Pancreas	Pancrea
32	chr4:130013400-130015200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr4:130013400-130015200	Active TSS	HSMMtube	muscle
34	chr4:130013400-130015400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:130013400-130015400	Active TSS	Colonic Mucosa	Colon
36	chr4:130013400-130015400	Active TSS	Fetal Intestine Large	intestine
37	chr4:130013400-130015400	Active TSS	Psoas Muscle	Psoas
38	chr4:130013400-130015400	Active TSS	Right Atrium	heart
39	chr4:130013400-130015400	Active TSS	Right Ventricle	heart
40	chr4:130013400-130015400	Active TSS	Thymus	Thymus
41	chr4:130013400-130015600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:130013400-130015600	Active TSS	Fetal Muscle Leg	muscle
43	chr4:130013400-130015800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr4:130013600-130015200	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr4:130013600-130015200	Active TSS	Brain Germinal Matrix	brain
46	chr4:130013600-130015200	Active TSS	Fetal Heart	heart
47	chr4:130013600-130015200	Active TSS	Placenta Amnion	Placenta Amnion
48	chr4:130013600-130015200	Active TSS	HSMM	muscle
49	chr4:130013600-130015400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:130013600-130015400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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