Variant report

Variant	rs62406695
Chromosome Location	chr5:179105523-179105524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:458)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:458 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr5:179104808-179105870	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:179104877-179106481	NB4	blood:	n/a	n/a
3	POLR2A	chr5:179104964-179105907	GM12878	blood:	n/a	n/a
4	MAX	chr5:179104845-179106370	SK-N-SH	brain:	n/a	n/a
5	TAF1	chr5:179105040-179106559	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:179105142-179106046	Gliobla	brain:	n/a	n/a
7	GTF2B	chr5:179105367-179105774	K562	blood:	n/a	n/a
8	REST	chr5:179104843-179106294	H1-neurons	neurons:	n/a	n/a
9	CEBPB	chr5:179104989-179106198	GM12878	blood:	n/a	chr5:179105576-179105587
10	USF1	chr5:179105376-179105723	SK-N-SH_RA	brain:	n/a	n/a
11	BRCA1	chr5:179105347-179105597	HepG2	liver:	n/a	n/a
12	FOXP2	chr5:179105317-179105826	SK-N-MC	brain:	n/a	n/a
13	CEBPB	chr5:179105322-179105918	K562	blood:	n/a	chr5:179105576-179105587
14	ELF1	chr5:179105219-179105629	A549	lung:	n/a	n/a
15	MYC	chr5:179104880-179105938	K562	blood:	n/a	n/a
16	POLR2A	chr5:179104629-179106368	GM12892	blood:	n/a	n/a
17	POLR2A	chr5:179105001-179106406	GM18951	blood:	n/a	n/a
18	IRF1	chr5:179104938-179105859	K562	blood:	n/a	n/a
19	EP300	chr5:179105091-179105768	K562	blood:	n/a	n/a
20	PML	chr5:179105320-179105907	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:179104865-179106343	GM12891	blood:	n/a	n/a
22	RCOR1	chr5:179105045-179105532	K562	blood:	n/a	n/a
23	RAD21	chr5:179105371-179105879	IMR90	lung:	n/a	n/a
24	RAD21	chr5:179105348-179105892	HepG2	liver:	n/a	n/a
25	MYC	chr5:179105259-179105865	K562	blood:	n/a	n/a
26	CTCF	chr5:179105498-179105794	HepG2	liver:	n/a	n/a
27	POLR2A	chr5:179104939-179106128	GM12892	blood:	n/a	n/a
28	POLR2A	chr5:179104608-179106366	PANC-1	pancreas:	n/a	n/a
29	MYBL2	chr5:179105077-179105797	HepG2	liver:	n/a	n/a
30	NRF1	chr5:179104975-179106195	SK-N-SH	brain:	n/a	chr5:179105631-179105642 chr5:179105555-179105569 chr5:179105555-179105564 chr5:179105555-179105566 chr5:179105554-179105565 chr5:179105552-179105566
31	USF2	chr5:179105156-179105760	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:179104995-179105982	HUVEC	blood vessel:	n/a	n/a
33	ATF3	chr5:179105413-179105815	K562	blood:	n/a	n/a
34	RUNX3	chr5:179104937-179106498	GM12878	blood:	n/a	n/a
35	ATF3	chr5:179105154-179105824	A549	lung:	n/a	n/a
36	BCL11A	chr5:179105356-179105544	GM12878	blood:	n/a	n/a
37	BACH1	chr5:179105168-179105658	H1-hESC	embryonic stem cell:	n/a	n/a
38	YY1	chr5:179105141-179105892	SK-N-SH_RA	brain:	n/a	n/a
39	JUN	chr5:179104730-179105981	K562	blood:	n/a	chr5:179105577-179105590
40	POLR2A	chr5:179105118-179105954	SK-N-MC	brain:	n/a	n/a
41	HDAC2	chr5:179105216-179105837	HepG2	liver:	n/a	chr5:179105555-179105564
42	PML	chr5:179105023-179105821	K562	blood:	n/a	n/a
43	POLR2A	chr5:179105038-179105834	HepG2	liver:	n/a	n/a
44	CTCF	chr5:179105211-179105861	K562	blood:	n/a	n/a
45	ATF2	chr5:179105100-179105843	GM12878	blood:	n/a	n/a
46	MAFK	chr5:179105142-179105754	K562	blood:	n/a	chr5:179105736-179105751
47	POLR2A	chr5:179105100-179105870	GM12891	blood:	n/a	n/a
48	POLR2A	chr5:179105049-179105866	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:179104809-179106482	PANC-1	pancreas:	n/a	n/a
50	FOXM1	chr5:179105082-179105619	GM12878	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179101962..179108661-chr5:179122383..179128408,19	MCF-7	breast:
2	chr5:179104081..179106481-chr5:179247871..179249548,2	K562	blood:
3	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
4	chr12:129308245..129308810-chr5:179105164..179105861,2	Hela-S3	cervix:
5	chr5:179049533..179052334-chr5:179104256..179107492,4	MCF-7	breast:
6	chr5:179104047..179107935-chr5:179157751..179161258,3	K562	blood:
7	chr5:179104105..179106791-chr5:179194829..179197317,2	K562	blood:
8	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
9	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
10	chr5:179047581..179051358-chr5:179102429..179108878,16	K562	blood:
11	chr5:179102368..179107935-chr5:179157286..179161555,5	K562	blood:
12	chr5:179104067..179106595-chr5:179220718..179223236,3	MCF-7	breast:
13	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
14	chr5:179104088..179107429-chr5:179222108..179224529,3	MCF-7	breast:
15	chr11:64084471..64085404-chr5:179105157..179106130,2	NB4	blood:
16	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:
17	chr5:178986726..178988892-chr5:179104044..179106638,2	K562	blood:
18	chr5:179032616..179037685-chr5:179101606..179106447,5	K562	blood:
19	chr5:179103716..179105834-chr5:179232132..179234075,2	MCF-7	breast:
20	chr1:32671254..32672166-chr5:179105011..179105570,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
CANX	TF binding region
HMGB3P22	TF binding region
ENSG00000127022	Chromatin interaction
ENSG00000224066	Chromatin interaction
ENSG00000173113	Chromatin interaction
ENSG00000160051	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000139370	Chromatin interaction
ENSG00000176783	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11749841	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4388174	0.81[AFR][1000 genomes]
rs4701195	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4701196	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57551480	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62406694	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6601065	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66902084	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72662129	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72662130	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72662131	0.84[AMR][1000 genomes];0.84[EUR][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	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
2	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
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 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	chr5:179103800-179105600	Active TSS	Hela-S3	cervix
2	chr5:179103800-179106400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:179104200-179105600	Active TSS	A549	lung
4	chr5:179104200-179105600	Active TSS	K562	blood
5	chr5:179104200-179106600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:179104400-179105600	Active TSS	Muscle Satellite Cultured Cells	--
7	chr5:179104400-179105600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:179104400-179105600	Active TSS	HepG2	liver
9	chr5:179104400-179105800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:179104400-179105800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:179104400-179105800	Active TSS	GM12878-XiMat	blood
12	chr5:179104400-179106400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr5:179104600-179105600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:179104600-179105600	Active TSS	HMEC	breast
15	chr5:179104600-179105800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr5:179104600-179105800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:179104600-179105800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:179104600-179105800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr5:179104600-179105800	Active TSS	Brain Hippocampus Middle	brain
20	chr5:179104600-179105800	Active TSS	Stomach Smooth Muscle	stomach
21	chr5:179104600-179105800	Active TSS	NHEK	skin
22	chr5:179104600-179106000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:179104600-179106000	Active TSS	Fetal Intestine Small	intestine
24	chr5:179104600-179106000	Active TSS	Fetal Stomach	stomach
25	chr5:179104600-179106200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:179104600-179106200	Active TSS	Brain Anterior Caudate	brain
27	chr5:179104600-179106200	Active TSS	HSMM	muscle
28	chr5:179104600-179106400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr5:179104600-179106400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr5:179104600-179106400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr5:179104600-179106400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:179104600-179106400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:179104600-179106400	Active TSS	Fetal Kidney	kidney
34	chr5:179104600-179106600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr5:179104600-179106600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr5:179104600-179106600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:179104600-179106600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr5:179104600-179106800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr5:179104800-179105600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:179104800-179105600	Active TSS	Fetal Lung	lung
41	chr5:179104800-179105600	Active TSS	NH-A	brain
42	chr5:179104800-179105800	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr5:179104800-179105800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:179104800-179105800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:179104800-179105800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:179104800-179105800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr5:179104800-179105800	Active TSS	Fetal Muscle Leg	muscle
48	chr5:179104800-179105800	Active TSS	Placenta	Placenta
49	chr5:179104800-179105800	Active TSS	Psoas Muscle	Psoas
50	chr5:179104800-179105800	Active TSS	Right Ventricle	heart

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