Variant report

Variant	rs13038143
Chromosome Location	chr20:52484888-52484889
allele	G/T
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52484717..52486672-chr20:52490016..52492250,2	K562	blood:
2	chr20:52484766..52486838-chr4:146637094..146638832,2	MCF-7	breast:
3	chr12:66506885..66508576-chr20:52484476..52487409,2	MCF-7	breast:
4	chr20:52483037..52485677-chr9:12813088..12815674,2	MCF-7	breast:
5	chr20:52481752..52485242-chr20:55845808..55850200,8	MCF-7	breast:
6	chr20:52484501..52486317-chr6:34526583..34529198,2	MCF-7	breast:
7	chr20:52238784..52241360-chr20:52484795..52486352,2	K562	blood:
8	chr19:10763818..10766592-chr20:52482564..52485159,2	MCF-7	breast:
9	chr17:57913904..57917268-chr20:52480979..52484930,6	MCF-7	breast:
10	chr20:52484799..52486540-chr20:52532724..52534997,2	K562	blood:
11	chr20:52478179..52488683-chr20:55835744..55846940,26	MCF-7	breast:
12	chr20:52483064..52485443-chr7:29327053..29329425,2	MCF-7	breast:
13	chr20:52484288..52486178-chr4:88957310..88959480,2	MCF-7	breast:
14	chr20:52471901..52491673-chr20:55835708..55845674,34	MCF-7	breast:
15	chr17:59530190..59532912-chr20:52483591..52486439,2	MCF-7	breast:
16	chr20:52480121..52486257-chr20:55824427..55830996,6	MCF-7	breast:
17	chr20:52483983..52486847-chr6:26156318..26159151,2	MCF-7	breast:
18	chr20:52483057..52485404-chr20:52528984..52531501,2	K562	blood:
19	chr17:57920817..57923301-chr20:52482910..52485730,2	MCF-7	breast:
20	chr20:52484120..52485037-chr3:64016477..64017091,2	MCF-7	breast:
21	chr20:52483421..52485868-chr20:55831559..55834264,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158373	Chromatin interaction
ENSG00000129351	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000241721	Chromatin interaction
ENSG00000267100	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000106069	Chromatin interaction
ENSG00000235448	Chromatin interaction
ENSG00000168298	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11086444	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11697016	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11699573	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11906676	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13037872	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859902	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35507231	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6064013	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6068699	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6068702	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8114312	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
6	esv18025	chr20:52464720-52486135	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
7	nsv586222	chr20:52473679-52506380	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	74 gene(s)	inside rSNPs	diseases
8	esv3378662	chr20:52474345-52485443	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	60 gene(s)	inside rSNPs	diseases
9	esv3341653	chr20:52474345-52485543	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	60 gene(s)	inside rSNPs	diseases
10	esv3381391	chr20:52474445-52485443	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	60 gene(s)	inside rSNPs	diseases
11	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
12	esv3382989	chr20:52475045-52485243	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	60 gene(s)	inside rSNPs	diseases
13	esv3353743	chr20:52476445-52485443	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	60 gene(s)	inside rSNPs	diseases
14	esv3395767	chr20:52476445-52485443	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	60 gene(s)	inside rSNPs	diseases
15	esv3323379	chr20:52484370-52486843	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
16	esv3403644	chr20:52484570-52487118	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
17	esv3419756	chr20:52484645-52486693	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52480000-52485000	Enhancers	H9 Cell Line	embryonic stem cell
2	chr20:52480000-52485000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr20:52480200-52485200	Enhancers	Primary B cells from peripheral blood	blood
4	chr20:52480200-52485200	Enhancers	Placenta	Placenta
5	chr20:52480800-52485000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:52481600-52485000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr20:52481800-52489200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:52482800-52485000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr20:52482800-52485800	Weak transcription	Left Ventricle	heart
10	chr20:52482800-52485800	Weak transcription	Ovary	ovary
11	chr20:52482800-52486000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr20:52482800-52486000	Weak transcription	Lung	lung
13	chr20:52482800-52486200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr20:52482800-52489200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr20:52482800-52489400	Weak transcription	Aorta	Aorta
16	chr20:52482800-52489800	Weak transcription	Esophagus	oesophagus
17	chr20:52482800-52492000	Weak transcription	Gastric	stomach
18	chr20:52483000-52485200	Enhancers	Fetal Thymus	thymus
19	chr20:52483200-52486200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr20:52483400-52485000	Enhancers	HMEC	breast
21	chr20:52483400-52485200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:52483400-52489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:52483400-52495000	Weak transcription	Spleen	Spleen
24	chr20:52483600-52485800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr20:52483600-52486200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr20:52483600-52486200	Weak transcription	Colon Smooth Muscle	Colon
27	chr20:52483600-52486200	Weak transcription	Hela-S3	cervix
28	chr20:52483600-52486200	Weak transcription	HUVEC	blood vessel
29	chr20:52483600-52490600	Weak transcription	Right Atrium	heart
30	chr20:52483800-52485800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr20:52483800-52486200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:52483800-52488200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:52483800-52488600	Weak transcription	NHLF	lung
34	chr20:52484000-52485200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr20:52484000-52485800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr20:52484000-52485800	Weak transcription	Dnd41	blood
37	chr20:52484000-52486000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:52484000-52486000	Weak transcription	Osteobl	bone
39	chr20:52484000-52486200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr20:52484000-52488000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:52484000-52488800	Weak transcription	HSMMtube	muscle
42	chr20:52484200-52485000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr20:52484200-52485000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr20:52484200-52486000	Weak transcription	Fetal Brain Male	brain
45	chr20:52484200-52488800	Weak transcription	Fetal Stomach	stomach
46	chr20:52484400-52485000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:52484400-52485000	Enhancers	Pancreas	Pancrea
48	chr20:52484400-52485000	Enhancers	HepG2	liver
49	chr20:52484400-52485800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr20:52484400-52485800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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