Variant report

Variant	rs6013809
Chromosome Location	chr20:52445989-52445990
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52367432..52369907-chr20:52444310..52447312,3	K562	blood:
2	chr20:52436875..52438996-chr20:52445815..52447419,2	K562	blood:
3	chr17:79479762..79482602-chr20:52444194..52446135,2	MCF-7	breast:
4	chr17:56735298..56737736-chr20:52444962..52446651,2	MCF-7	breast:
5	chr20:52445461..52447922-chr22:31741028..31743008,2	MCF-7	breast:
6	chr19:12904144..12906645-chr20:52443752..52446655,2	MCF-7	breast:
7	chr20:52445630..52448175-chr20:52453269..52455432,3	K562	blood:
8	chr1:116005229..116007431-chr20:52444362..52446929,2	MCF-7	breast:
9	chr17:57917840..57922874-chr20:52444092..52449259,5	MCF-7	breast:
10	chr20:52444427..52449219-chr20:55839929..55843430,6	MCF-7	breast:
11	chr20:52444977..52447125-chr9:74381841..74383738,2	MCF-7	breast:
12	chr20:52445950..52448025-chr20:52488646..52490930,2	K562	blood:
13	chr17:56708142..56710971-chr20:52444323..52447306,3	MCF-7	breast:
14	chr20:52445801..52446657-chr9:91933423..91933972,2	Hela-S3	cervix:
15	chr20:52445220..52447050-chr21:41755084..41757495,2	MCF-7	breast:
16	chr10:30096097..30096629-chr20:52445803..52446599,2	Hela-S3	cervix:
17	chr17:56735072..56736721-chr20:52444117..52446150,2	MCF-7	breast:
18	chr20:52369629..52371487-chr20:52444483..52447130,3	K562	blood:
19	chr20:52445412..52448214-chr20:52672686..52675334,2	MCF-7	breast:
20	chr1:115052548..115055382-chr20:52445896..52448449,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226308	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000229947	Chromatin interaction
ENSG00000187742	Chromatin interaction
ENSG00000100105	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000229848	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000135048	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11086442	0.88[ASN][1000 genomes]
rs11698816	0.85[ASN][1000 genomes]
rs2097849	0.85[EUR][1000 genomes]
rs2215403	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs4809939	0.80[EUR][1000 genomes]
rs4809942	0.81[JPT][hapmap]
rs4811472	0.84[CEU][hapmap]
rs4811474	0.80[EUR][1000 genomes]
rs4811475	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6022761	0.84[CEU][hapmap]
rs6022766	0.84[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs6022767	0.84[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs6022779	0.88[CEU][hapmap];0.94[YRI][hapmap];0.89[EUR][1000 genomes]
rs6022782	0.84[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6022786	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6064007	0.83[EUR][1000 genomes]
rs6064008	0.83[EUR][1000 genomes]
rs6064011	0.84[CEU][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap]
rs6068679	0.82[EUR][1000 genomes]
rs6068680	0.82[EUR][1000 genomes]
rs6068681	0.89[EUR][1000 genomes]
rs6068684	0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6068691	0.81[JPT][hapmap]
rs6091748	0.88[CEU][hapmap]
rs6097618	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs6097632	0.81[JPT][hapmap]
rs6123320	0.81[ASN][1000 genomes]
rs6126982	0.85[JPT][hapmap]

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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers 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	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52441200-52446000	Enhancers	HepG2	liver
3	chr20:52443400-52456000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:52443600-52447000	Enhancers	Placenta	Placenta
5	chr20:52443600-52447200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr20:52443800-52446800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr20:52443800-52449000	Weak transcription	Lung	lung
8	chr20:52444000-52446000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:52444000-52453200	Weak transcription	Small Intestine	intestine
10	chr20:52444200-52446200	Enhancers	Brain Germinal Matrix	brain
11	chr20:52444400-52446000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:52444400-52446000	Flanking Active TSS	Fetal Kidney	kidney
13	chr20:52444400-52446000	Flanking Active TSS	HMEC	breast
14	chr20:52444400-52446600	Active TSS	NHDF-Ad	bronchial
15	chr20:52444400-52446800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:52444400-52446800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr20:52444400-52446800	Active TSS	Stomach Smooth Muscle	stomach
18	chr20:52444400-52447000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:52444400-52447000	Flanking Active TSS	Hela-S3	cervix
20	chr20:52444400-52447000	Flanking Active TSS	HUVEC	blood vessel
21	chr20:52444400-52447000	Flanking Active TSS	NHEK	skin
22	chr20:52444600-52446600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr20:52444600-52446600	Active TSS	Aorta	Aorta
24	chr20:52444600-52446800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr20:52444600-52447000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr20:52444600-52447000	Active TSS	Right Atrium	heart
27	chr20:52444800-52446000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr20:52444800-52446000	Flanking Active TSS	Osteobl	bone
29	chr20:52444800-52446800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr20:52444800-52446800	Flanking Active TSS	NH-A	brain
31	chr20:52444800-52447000	Active TSS	Psoas Muscle	Psoas
32	chr20:52444800-52447200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr20:52444800-52456000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr20:52445000-52446000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr20:52445000-52446000	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr20:52445000-52446200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr20:52445000-52446200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr20:52445000-52446200	Active TSS	Ovary	ovary
39	chr20:52445000-52446400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr20:52445000-52446400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr20:52445000-52446400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr20:52445000-52446400	Active TSS	Brain Anterior Caudate	brain
43	chr20:52445000-52446800	Enhancers	Fetal Heart	heart
44	chr20:52445000-52446800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr20:52445000-52447000	Active TSS	Brain Hippocampus Middle	brain
46	chr20:52445000-52447000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr20:52445000-52447000	Flanking Active TSS	K562	blood
48	chr20:52445000-52447200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr20:52445000-52447200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr20:52445200-52446000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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