Variant report

Variant	rs72824534
Chromosome Location	chr5:179035080-179035081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179033696-179035774	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:179033876-179035743	GM12878	blood:	n/a	n/a
3	BCL3	chr5:179032107-179035783	A549	lung:	n/a	chr5:179035483-179035490
4	POLR2A	chr5:179034219-179035551	GM18526	blood:	n/a	n/a
5	PBX3	chr5:179032834-179035705	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:179033210-179035823	MCF-7	breast:	n/a	n/a
7	POLR2A	chr5:179032245-179039419	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:179033899-179035135	ProgFib	skin:	n/a	n/a
9	POLR2A	chr5:179033919-179035886	HL-60	blood:	n/a	n/a
10	POLR2A	chr5:179032268-179046451	HepG2	liver:	n/a	n/a
11	BCL3	chr5:179032261-179035749	A549	lung:	n/a	chr5:179035483-179035490
12	POLR2A	chr5:179033852-179035553	GM18951	blood:	n/a	n/a
13	POLR2A	chr5:179033428-179035696	GM12878	blood:	n/a	n/a
14	HEY1	chr5:179033519-179035673	HepG2	liver:	n/a	n/a
15	POLR2A	chr5:179032506-179042560	K562	blood:	n/a	n/a
16	GATA3	chr5:179034330-179035683	A549	lung:	n/a	n/a
17	JUND	chr5:179032740-179035812	A549	lung:	n/a	n/a
18	POLR2A	chr5:179032550-179042176	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:179032925-179035665	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:179032463-179035765	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr5:179032318-179035908	U87	brain:	n/a	n/a
22	POLR2A	chr5:179032942-179037625	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr5:179032822-179035715	A549	lung:	n/a	n/a
24	POLR2A	chr5:179033713-179035707	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:179032199-179035786	ECC-1	luminal epithelium:	n/a	n/a
26	PBX3	chr5:179034239-179035518	A549	lung:	n/a	n/a
27	POLR2A	chr5:179033397-179039296	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr5:179032846-179039303	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr5:179032115-179039357	H1-hESC	embryonic stem cell:	n/a	n/a
30	RFX5	chr5:179034982-179035276	HepG2	liver:	n/a	n/a
31	ZC3H11A	chr5:179035012-179035197	K562	blood:	n/a	n/a
32	POLR2A	chr5:179033868-179035804	K562	blood:	n/a	n/a
33	POLR2A	chr5:179034028-179035576	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:179033118-179035822	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr5:179032271-179039347	GM12892	blood:	n/a	n/a
36	POLR2A	chr5:179032412-179035825	K562	blood:	n/a	n/a
37	POLR2A	chr5:179033806-179035870	HL-60	blood:	n/a	n/a
38	POLR2A	chr5:179032390-179035771	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr5:179033701-179035801	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr5:179033643-179035717	U87	brain:	n/a	n/a
41	POLR2A	chr5:179032232-179039282	SK-N-SH	brain:	n/a	n/a
42	TCF12	chr5:179032525-179035096	A549	lung:	n/a	chr5:179032806-179032813 chr5:179035039-179035049
43	POLR2A	chr5:179033643-179035699	U87	brain:	n/a	n/a
44	POLR2A	chr5:179033963-179035660	Hela-S3	cervix:	n/a	n/a
45	NFATC1	chr5:179034227-179035774	GM12878	blood:	n/a	n/a
46	FOSL2	chr5:179034972-179035591	HepG2	liver:	n/a	n/a
47	REST	chr5:179034358-179035250	A549	lung:	n/a	n/a
48	POLR2A	chr5:179034265-179035655	HepG2	liver:	n/a	n/a
49	POLR2A	chr5:179033606-179035658	K562	blood:	n/a	n/a
50	POLR2A	chr5:179032426-179035785	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179034167..179038139-chr5:179125249..179127406,3	MCF-7	breast:
2	chr5:179011616..179013589-chr5:179034982..179036835,2	K562	blood:
3	chr5:179032616..179037685-chr5:179101606..179106447,5	K562	blood:
4	chr5:178977786..178979426-chr5:179034377..179036476,2	MCF-7	breast:
5	chr5:179034995..179037887-chr5:179124544..179128614,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244945	TF binding region
ENSG00000176783	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs4700813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700817	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4701135	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701144	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58828813	0.91[ASN][1000 genomes]
rs72822602	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72824510	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72824515	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72824520	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824522	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824524	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824531	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72824532	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824544	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72824556	0.84[ASN][1000 genomes]
rs73809617	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
4	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
5	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 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	chr5:178987200-179040800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:178987600-179045600	Strong transcription	Fetal Intestine Small	intestine
3	chr5:178987800-179045600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:179002200-179045600	Strong transcription	Fetal Intestine Large	intestine
5	chr5:179007400-179035200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:179007400-179035200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:179007400-179037400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:179007400-179040200	Strong transcription	Placenta	Placenta
9	chr5:179007400-179045000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:179011000-179045600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:179011200-179039000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:179011200-179043800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:179012400-179036400	Strong transcription	Lung	lung
14	chr5:179012600-179037600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:179012600-179047000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr5:179012800-179039000	Strong transcription	Left Ventricle	heart
17	chr5:179012800-179040000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr5:179013600-179037800	Strong transcription	Fetal Stomach	stomach
19	chr5:179013800-179035400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:179013800-179044800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:179014000-179042000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:179014000-179044400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:179014000-179046000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:179016000-179041800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:179016200-179045000	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr5:179018400-179035400	Strong transcription	Brain Germinal Matrix	brain
27	chr5:179023200-179037800	Weak transcription	Fetal Heart	heart
28	chr5:179023400-179037800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:179025200-179045000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:179026600-179036800	Weak transcription	K562	blood
31	chr5:179026600-179040600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:179027600-179039600	Weak transcription	Small Intestine	intestine
33	chr5:179028200-179046200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr5:179028400-179046000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:179028600-179046200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:179028800-179037800	Strong transcription	NHLF	lung
37	chr5:179028800-179045000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr5:179029000-179035200	Strong transcription	NHEK	skin
39	chr5:179029000-179038800	Strong transcription	Fetal Lung	lung
40	chr5:179029200-179045600	Strong transcription	Primary B cells from cord blood	blood
41	chr5:179030000-179037400	Weak transcription	Psoas Muscle	Psoas
42	chr5:179030000-179040800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:179030600-179036800	Weak transcription	HSMMtube	muscle
44	chr5:179031000-179041000	Genic enhancers	Fetal Muscle Leg	muscle
45	chr5:179031000-179045600	Strong transcription	Osteobl	bone
46	chr5:179031000-179046200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:179031200-179036400	Strong transcription	Spleen	Spleen
48	chr5:179032200-179035600	Genic enhancers	Brain Hippocampus Middle	brain
49	chr5:179032200-179038800	Strong transcription	Pancreas	Pancrea
50	chr5:179032200-179039200	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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