Variant report

Variant	rs852478
Chromosome Location	chr7:5639233-5639234
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:5638947-5639757	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr7:5637211-5639498	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:5637379-5639819	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:5637526-5639628	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:5638952-5639270	GM12891	blood:	n/a	n/a
6	POLR2A	chr7:5638595-5639312	GM12891	blood:	n/a	n/a
7	POLR2A	chr7:5637304-5639803	K562	blood:	n/a	n/a
8	POLR2A	chr7:5637367-5640337	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:5638907-5639567	H1-hESC	embryonic stem cell:	n/a	n/a
10	HEY1	chr7:5639203-5639399	K562	blood:	n/a	n/a
11	POLR2A	chr7:5638718-5639257	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr7:5639145-5639512	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr7:5637303-5639725	K562	blood:	n/a	n/a
14	POLR2A	chr7:5637343-5639771	K562	blood:	n/a	n/a
15	POLR2A	chr7:5637357-5639626	GM12892	blood:	n/a	n/a
16	POLR2A	chr7:5638909-5639261	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr7:5638980-5639268	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr7:5637621-5639234	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:5637301-5639851	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:5637497-5639744	GM12892	blood:	n/a	n/a
21	POLR2A	chr7:5637423-5639596	K562	blood:	n/a	n/a
22	POLR2A	chr7:5639222-5639518	HepG2	liver:	n/a	n/a
23	POLR2A	chr7:5637301-5639802	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:5596314..5597931-chr7:5637976..5640574,2	MCF-7	breast:
2	chr7:5561309..5562941-chr7:5638021..5639699,2	K562	blood:
3	chr7:5601967..5603891-chr7:5638384..5639932,2	MCF-7	breast:
4	chr7:5638174..5640538-chr7:5702436..5704254,2	K562	blood:
5	chr7:5637430..5639674-chr7:5702754..5705008,2	K562	blood:
6	chr7:5563317..5574038-chr7:5630450..5643029,58	K562	blood:
7	chr7:5464118..5465697-chr7:5637454..5640085,2	K562	blood:
8	chr7:5637583..5639274-chr7:5662917..5664580,2	MCF-7	breast:

No data

Variant related genes	Relation type
FSCN1	TF binding region
ENSG00000272953	Chromatin interaction
ENSG00000182095	Chromatin interaction
ENSG00000263900	Chromatin interaction
ENSG00000272719	Chromatin interaction
ENSG00000075624	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1640236	0.84[AFR][1000 genomes]
rs1640238	0.84[AFR][1000 genomes]
rs1725182	0.84[AFR][1000 genomes]
rs2966446	0.81[AFR][1000 genomes]
rs2966447	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55718102	0.83[EUR][1000 genomes]
rs55804712	0.81[EUR][1000 genomes]
rs56113524	0.83[EUR][1000 genomes]
rs852479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	333 gene(s)	inside rSNPs	diseases
5	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
6	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
7	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
8	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
9	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
10	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
11	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
12	nsv1025434	chr7:5537571-5705283	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
13	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
14	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
15	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
16	nsv887414	chr7:5584934-5667645	Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
17	nsv887415	chr7:5584934-5675305	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
18	nsv887416	chr7:5584934-5695259	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
19	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
20	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
21	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5634400-5639600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:5634800-5640200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:5635600-5639400	Enhancers	Spleen	Spleen
4	chr7:5635800-5642800	Weak transcription	Aorta	Aorta
5	chr7:5636000-5639800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:5636200-5639600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr7:5636200-5642600	Weak transcription	HepG2	liver
8	chr7:5636200-5662000	Weak transcription	Fetal Kidney	kidney
9	chr7:5636400-5639600	Genic enhancers	Fetal Stomach	stomach
10	chr7:5636400-5639600	Enhancers	Ovary	ovary
11	chr7:5636400-5639800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:5636400-5640200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:5636400-5642600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:5636600-5639600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr7:5636600-5640000	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr7:5636600-5643400	Weak transcription	Pancreas	Pancrea
17	chr7:5636600-5661400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr7:5636800-5639400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:5636800-5639800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr7:5636800-5639800	Enhancers	Brain Substantia Nigra	brain
21	chr7:5636800-5640000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:5636800-5643200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:5636800-5661200	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:5637400-5639600	Transcr. at gene 5' and 3'	NHEK	skin
25	chr7:5637400-5639800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:5637600-5639800	Enhancers	Fetal Heart	heart
27	chr7:5637800-5639600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:5638000-5639800	Genic enhancers	NH-A	brain
29	chr7:5638000-5640200	Enhancers	Brain Anterior Caudate	brain
30	chr7:5638200-5639400	Genic enhancers	Fetal Intestine Small	intestine
31	chr7:5638200-5639800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:5638200-5639800	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr7:5638200-5639800	Genic enhancers	HMEC	breast
34	chr7:5638400-5639600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:5638400-5639600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr7:5638400-5639600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:5638400-5639600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:5638400-5639600	Enhancers	Brain Cingulate Gyrus	brain
39	chr7:5638400-5639800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:5638400-5639800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr7:5638400-5642800	Weak transcription	Brain Angular Gyrus	brain
42	chr7:5638400-5648200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:5638400-5659000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:5638600-5639400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:5638600-5639400	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr7:5638600-5642000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr7:5638600-5643400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:5638800-5639600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
49	chr7:5638800-5639600	Genic enhancers	Brain Germinal Matrix	brain
50	chr7:5638800-5639800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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