Variant report

Variant	rs72824528
Chromosome Location	chr5:179032469-179032470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr5:179032107-179035783	A549	lung:	n/a	chr5:179035483-179035490
2	POLR2A	chr5:179032245-179039419	GM12892	blood:	n/a	n/a
3	POLR2A	chr5:179032268-179046451	HepG2	liver:	n/a	n/a
4	BCL3	chr5:179032261-179035749	A549	lung:	n/a	chr5:179035483-179035490
5	POLR2A	chr5:179032442-179032852	GM12878	blood:	n/a	n/a
6	CTCF	chr5:179032360-179032510	BJ	skin:	n/a	n/a
7	POLR2A	chr5:179032463-179035765	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr5:179032318-179035908	U87	brain:	n/a	n/a
9	POLR2A	chr5:179032199-179035786	ECC-1	luminal epithelium:	n/a	n/a
10	FOXA2	chr5:179032134-179032621	A549	lung:	n/a	n/a
11	POLR2A	chr5:179032115-179039357	H1-hESC	embryonic stem cell:	n/a	n/a
12	USF2	chr5:179032467-179033154	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr5:179032340-179032490	NHDF-neo	bronchial:	n/a	n/a
14	POLR2A	chr5:179032302-179032843	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr5:179032271-179039347	GM12892	blood:	n/a	n/a
16	POLR2A	chr5:179032412-179035825	K562	blood:	n/a	n/a
17	POLR2A	chr5:179032390-179035771	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr5:179032232-179039282	SK-N-SH	brain:	n/a	n/a
19	FOXA1	chr5:179032240-179032577	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:179032461-179032748	A549	lung:	n/a	n/a
21	POLR2A	chr5:179032378-179032812	A549	lung:	n/a	n/a
22	POLR2A	chr5:179032429-179032779	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr5:179032426-179035785	HepG2	liver:	n/a	n/a
24	POLR2A	chr5:179032422-179032602	K562	blood:	n/a	n/a
25	POLR2A	chr5:179031954-179039309	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr5:179032289-179041224	A549	lung:	n/a	n/a
27	POLR2A	chr5:179032451-179035881	GM12891	blood:	n/a	n/a
28	FOXA2	chr5:179032081-179032739	A549	lung:	n/a	n/a
29	FOXA2	chr5:179032242-179032537	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:179032422-179032785	K562	blood:	n/a	n/a
31	POLR2A	chr5:179032003-179035848	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr5:179032422-179032721	A549	lung:	n/a	n/a
33	POLR2A	chr5:179032423-179032777	GM12878	blood:	n/a	n/a
34	FOXA1	chr5:179032260-179032511	T-47D	breast:	n/a	n/a
35	POLR2A	chr5:179032235-179035778	IMR90	lung:	n/a	n/a
36	POLR2A	chr5:179032253-179032487	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr5:179032362-179041282	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr5:179032398-179042103	HepG2	liver:	n/a	n/a
39	POLR2A	chr5:179032210-179035908	U87	brain:	n/a	n/a
40	CTCF	chr5:179032460-179032610	NHDF-neo	bronchial:	n/a	n/a
41	POLR2A	chr5:179030899-179046584	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr5:179032324-179032569	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr5:179032177-179035793	SK-N-SH	brain:	n/a	n/a
44	FOXA1	chr5:179032252-179032496	HepG2	liver:	n/a	n/a
45	POLR2A	chr5:179032226-179041408	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr5:179032426-179039283	GM12878	blood:	n/a	n/a
47	POLR2A	chr5:179032181-179042621	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:179032235-179039304	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179023883..179026184-chr5:179031149..179032775,2	MCF-7	breast:
2	chr5:178951884..178954426-chr5:179031332..179033126,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244945	TF binding region
RUFY1	TF binding region

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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700817	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4701135	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701144	0.96[AFR][1000 genomes];0.97[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];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72824510	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72824515	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72824520	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824522	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824524	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824531	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72824532	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824544	0.82[AMR][1000 genomes];0.85[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	chr5:178996800-179034000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:178999800-179034800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:179000000-179034200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:179002200-179045600	Strong transcription	Fetal Intestine Large	intestine
8	chr5:179007400-179033800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:179007400-179034800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:179007400-179035200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:179007400-179035200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:179007400-179037400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:179007400-179040200	Strong transcription	Placenta	Placenta
14	chr5:179007400-179045000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:179007600-179034400	Strong transcription	Thymus	Thymus
16	chr5:179008200-179032800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr5:179010000-179034600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:179010800-179034000	Strong transcription	Fetal Thymus	thymus
19	chr5:179011000-179034200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:179011000-179045600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:179011200-179034000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr5:179011200-179039000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:179011200-179043800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:179012200-179034600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:179012200-179035000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:179012400-179034000	Strong transcription	Fetal Brain Female	brain
27	chr5:179012400-179036400	Strong transcription	Lung	lung
28	chr5:179012600-179037600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:179012600-179047000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr5:179012800-179034600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:179012800-179039000	Strong transcription	Left Ventricle	heart
32	chr5:179012800-179040000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr5:179013000-179034200	Strong transcription	Primary T cells from cord blood	blood
34	chr5:179013600-179037800	Strong transcription	Fetal Stomach	stomach
35	chr5:179013800-179035400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:179013800-179044800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:179014000-179042000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:179014000-179044400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:179014000-179046000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:179014200-179034200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:179016000-179041800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:179016200-179045000	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr5:179018400-179034400	Strong transcription	Dnd41	blood
44	chr5:179018400-179035400	Strong transcription	Brain Germinal Matrix	brain
45	chr5:179018600-179032600	Strong transcription	Brain Anterior Caudate	brain
46	chr5:179018600-179033000	Strong transcription	Gastric	stomach
47	chr5:179019200-179033200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:179019200-179035000	Strong transcription	Ovary	ovary
49	chr5:179021000-179034800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:179022000-179034600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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