Variant report

Variant	rs4809942
Chromosome Location	chr20:52463522-52463523
allele	A/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:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52455023..52457769-chr20:52462367..52464597,2	K562	blood:
2	chr20:52463385..52464295-chr9:123818115..123818641,2	MCF-7	breast:
3	chr20:52446291..52448679-chr20:52463374..52466298,2	K562	blood:
4	chr17:57921460..57923529-chr20:52462439..52464295,2	MCF-7	breast:
5	chr17:57915298..57917476-chr20:52461832..52464113,2	MCF-7	breast:
6	chr20:52462638..52464808-chr3:62850144..62851891,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSHZ2-4	chr20:52463387-52463584	XLOC_013570
2	lnc-TSHZ2-4	chr20:52463253-52463584	NONHSAT080405

No data

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10432728	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4809941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811476	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6013809	0.81[JPT][hapmap]
rs6022786	0.81[JPT][hapmap]
rs6022793	0.81[ASN][1000 genomes]
rs6064011	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6068688	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6068690	0.85[ASN][1000 genomes]
rs6068691	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6097618	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs6097632	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126982	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6126985	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126986	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720387	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52450400-52465200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr20:52450600-52465200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr20:52451200-52464000	Weak transcription	HSMM	muscle
4	chr20:52452400-52463800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr20:52452400-52465200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:52453600-52480200	Weak transcription	Small Intestine	intestine
7	chr20:52454400-52464200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr20:52455000-52464800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr20:52456600-52463800	Weak transcription	Fetal Lung	lung
10	chr20:52456600-52468400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr20:52456600-52476200	Weak transcription	Gastric	stomach
12	chr20:52458400-52464000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr20:52458400-52466200	Enhancers	Fetal Thymus	thymus
14	chr20:52458800-52465200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr20:52459000-52466600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr20:52459400-52464400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr20:52459400-52465200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr20:52459600-52463600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr20:52459600-52464000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr20:52459600-52468400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr20:52459600-52472600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr20:52459800-52463800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr20:52460200-52463800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr20:52461200-52463800	Enhancers	Thymus	Thymus
25	chr20:52461600-52463600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:52461600-52464000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr20:52461600-52464200	Enhancers	NHEK	skin
28	chr20:52462000-52464000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr20:52462000-52464600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr20:52462400-52465000	Enhancers	HepG2	liver
31	chr20:52462600-52464000	Enhancers	HMEC	breast
32	chr20:52462600-52464400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:52462800-52463600	Enhancers	Primary B cells from cord blood	blood
34	chr20:52462800-52463600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr20:52462800-52468200	Weak transcription	Osteobl	bone
36	chr20:52463000-52464000	Enhancers	Primary B cells from peripheral blood	blood
37	chr20:52463000-52468400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr20:52463000-52474000	Weak transcription	A549	lung
39	chr20:52463200-52463600	Enhancers	Spleen	Spleen
40	chr20:52463200-52463800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:52463200-52464800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr20:52463200-52465200	Enhancers	Primary hematopoietic stem cells	blood
43	chr20:52463200-52465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:52463200-52465200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr20:52463400-52463600	Flanking Active TSS	Dnd41	blood
46	chr20:52463400-52463600	Enhancers	GM12878-XiMat	blood
47	chr20:52463400-52464400	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr20:52463400-52464800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr20:52463400-52464800	Enhancers	Brain Anterior Caudate	brain
50	chr20:52463400-52465000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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