Variant report

Variant	rs56963754
Chromosome Location	chr4:8178988-8178989
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	MAFK	chr4:8178656-8179208	Hela-S3	cervix:	n/a	n/a
2	WRNIP1	chr4:8178569-8179004	GM12878	blood:	n/a	n/a
3	CTCF	chr4:8178292-8179099	A549	lung:	n/a	chr4:8178717-8178735
4	CTCF	chr4:8178481-8179034	MCF-7	breast:	n/a	chr4:8178717-8178735
5	CTCF	chr4:8178268-8179147	HCT-116	colon:	n/a	chr4:8178717-8178735
6	CTCF	chr4:8178472-8179037	HCT-116	colon:	n/a	chr4:8178717-8178735
7	RAD21	chr4:8178453-8179050	H1-hESC	embryonic stem cell:	n/a	chr4:8178856-8178869
8	RAD21	chr4:8178266-8179736	SK-N-SH	brain:	n/a	chr4:8178856-8178869
9	SMC3	chr4:8178532-8178999	Hela-S3	cervix:	n/a	n/a
10	RAD21	chr4:8178473-8178994	ECC-1	luminal epithelium:	n/a	chr4:8178856-8178869
11	CTCF	chr4:8178096-8179336	SK-N-SH	brain:	n/a	chr4:8178717-8178735
12	RAD21	chr4:8178452-8179014	SK-N-SH_RA	brain:	n/a	chr4:8178856-8178869
13	RAD21	chr4:8178294-8179177	HCT-116	colon:	n/a	chr4:8178856-8178869
14	RAD21	chr4:8178264-8179148	HCT-116	colon:	n/a	chr4:8178856-8178869
15	RAD21	chr4:8178469-8178999	H1-hESC	embryonic stem cell:	n/a	chr4:8178856-8178869
16	RAD21	chr4:8178504-8179036	A549	lung:	n/a	chr4:8178856-8178869
17	RAD21	chr4:8178537-8178989	Hela-S3	cervix:	n/a	chr4:8178856-8178869
18	ZNF263	chr4:8178426-8179004	HEK293-T-REx	kidney:	n/a	n/a
19	RAD21	chr4:8178396-8179036	MCF-7	breast:	n/a	chr4:8178856-8178869
20	SMC3	chr4:8178292-8179576	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr4:8178332-8179026	GM12878	blood:	n/a	chr4:8178717-8178735

No.	Distal block	Cell Line	Cell type
1	chr4:8177238..8179444-chr4:8182727..8185122,2	MCF-7	breast:
2	chr4:8178131..8179114-chr4:8239846..8240964,9	MCF-7	breast:
3	chr4:8178683..8179355-chr4:8239861..8240827,2	K562	blood:
4	chr4:8178210..8179173-chr4:8194105..8195549,8	MCF-7	breast:
5	chr4:8178298..8179365-chr4:8239616..8240695,4	MCF-7	breast:
6	chr4:8177372..8179736-chr4:8243215..8245049,2	K562	blood:
7	chr4:8158932..8160891-chr4:8178387..8181198,2	MCF-7	breast:
8	chr4:8178126..8179213-chr4:8194505..8195435,5	MCF-7	breast:
9	chr4:8178239..8179222-chr4:8243368..8244103,2	K562	blood:
10	chr4:8178129..8181116-chr4:8187357..8190314,2	K562	blood:

Variant related genes	Relation type
SH3TC1	TF binding region
ENSG00000163995	Chromatin interaction
ENSG00000125089	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11547949	0.91[AMR][1000 genomes]
rs2176437	0.82[AFR][1000 genomes]
rs28370452	0.91[AMR][1000 genomes]
rs28396639	0.91[AMR][1000 genomes]
rs28398157	0.91[AMR][1000 genomes]
rs28407374	0.91[AMR][1000 genomes]
rs28417837	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28480201	0.91[AMR][1000 genomes]
rs28572135	0.91[AMR][1000 genomes]
rs28580669	0.91[AMR][1000 genomes]
rs28650262	0.83[AMR][1000 genomes]
rs28716092	0.91[AMR][1000 genomes]
rs34412622	0.87[AFR][1000 genomes]
rs59775110	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73800408	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878591	chr4:8063501-8207083	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv878593	chr4:8125788-8233341	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv461216	chr4:8154534-8276411	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
6	nsv593626	chr4:8154534-8276411	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv878594	chr4:8154534-8286916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv470012	chr4:8171401-8233341	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv878596	chr4:8171401-8254784	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8170600-8183200	Weak transcription	Right Atrium	heart
2	chr4:8172400-8181600	Weak transcription	Esophagus	oesophagus
3	chr4:8176000-8190200	Weak transcription	Psoas Muscle	Psoas
4	chr4:8177400-8181000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:8178200-8179000	Enhancers	Right Ventricle	heart
6	chr4:8178400-8179000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr4:8178400-8179000	Enhancers	Primary B cells from peripheral blood	blood
8	chr4:8178400-8179000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr4:8178400-8179200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:8178400-8179200	Enhancers	Brain Anterior Caudate	brain
11	chr4:8178400-8179200	Enhancers	Fetal Heart	heart
12	chr4:8178400-8179200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr4:8178400-8179200	Enhancers	Thymus	Thymus
14	chr4:8178400-8179200	Enhancers	Spleen	Spleen
15	chr4:8178400-8179800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr4:8178400-8179800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr4:8178400-8179800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr4:8178400-8179800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr4:8178400-8179800	Enhancers	Fetal Muscle Leg	muscle
20	chr4:8178400-8179800	Enhancers	Fetal Thymus	thymus
21	chr4:8178400-8179800	Enhancers	Dnd41	blood
22	chr4:8178400-8180000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:8178600-8179000	Enhancers	Fetal Stomach	stomach
24	chr4:8178600-8185000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:8178800-8179000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr4:8178800-8179000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr4:8178800-8179000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:8178800-8179000	Enhancers	Fetal Intestine Large	intestine
29	chr4:8178800-8179000	Enhancers	Fetal Intestine Small	intestine
30	chr4:8178800-8179000	Enhancers	Left Ventricle	heart
31	chr4:8178800-8179000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr4:8178800-8179000	Enhancers	Stomach Mucosa	stomach
33	chr4:8178800-8179200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:8178800-8179200	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr4:8178800-8179400	Enhancers	Primary hematopoietic stem cells	blood
36	chr4:8178800-8179400	Enhancers	Hela-S3	cervix
37	chr4:8178800-8182200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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