Variant report

Variant	rs6097620
Chromosome Location	chr20:52455093-52455094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:45981222..45982758-chr20:52453760..52455443,2	MCF-7	breast:
2	chr17:57920608..57923011-chr20:52454169..52456607,2	MCF-7	breast:
3	chr20:52455023..52457769-chr20:52462367..52464597,2	K562	blood:
4	chr20:52445630..52448175-chr20:52453269..52455432,3	K562	blood:

Variant related genes	Relation type
ENSG00000101040	Chromatin interaction
ENSG00000231119	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs6091757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6091760	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097621	1.00[AFR][1000 genomes]
rs6097622	0.89[AFR][1000 genomes]
rs6097623	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097626	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097633	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097634	0.82[AFR][1000 genomes]
rs7261242	1.00[AFR][1000 genomes];1.00[AMR][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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52443400-52456000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52444800-52456000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:52446600-52455400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr20:52447000-52456000	Weak transcription	Placenta	Placenta
6	chr20:52447400-52456200	Weak transcription	HUVEC	blood vessel
7	chr20:52447400-52459400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr20:52449200-52456000	Weak transcription	Lung	lung
9	chr20:52449200-52456200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr20:52449600-52457800	Enhancers	Primary B cells from cord blood	blood
11	chr20:52449800-52461000	Enhancers	Primary B cells from peripheral blood	blood
12	chr20:52450000-52462000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr20:52450400-52457800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr20:52450400-52465200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr20:52450600-52465200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr20:52450800-52456000	Weak transcription	Fetal Muscle Leg	muscle
17	chr20:52451000-52456000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:52451000-52456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr20:52451000-52456200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:52451000-52457000	Weak transcription	NHDF-Ad	bronchial
21	chr20:52451000-52462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:52451200-52457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr20:52451200-52457200	Weak transcription	NHEK	skin
24	chr20:52451200-52464000	Weak transcription	HSMM	muscle
25	chr20:52452200-52456800	Enhancers	Fetal Intestine Large	intestine
26	chr20:52452400-52455200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr20:52452400-52455200	Weak transcription	Thymus	Thymus
28	chr20:52452400-52456000	Weak transcription	Spleen	Spleen
29	chr20:52452400-52463800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr20:52452400-52465200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr20:52452600-52455200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:52452600-52455800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr20:52452600-52461400	Weak transcription	Osteobl	bone
34	chr20:52453400-52456800	Enhancers	Fetal Intestine Small	intestine
35	chr20:52453600-52456000	Enhancers	HepG2	liver
36	chr20:52453600-52457200	Enhancers	Stomach Mucosa	stomach
37	chr20:52453600-52458000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr20:52453600-52480200	Weak transcription	Small Intestine	intestine
39	chr20:52453800-52455400	Weak transcription	Colonic Mucosa	Colon
40	chr20:52454000-52456000	Weak transcription	A549	lung
41	chr20:52454200-52456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr20:52454400-52457000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr20:52454400-52464200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr20:52454600-52455200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr20:52454600-52456200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr20:52454800-52457400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr20:52454800-52457400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr20:52454800-52457800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr20:52455000-52455200	Enhancers	Duodenum Mucosa	Duodenum
50	chr20:52455000-52455200	Enhancers	Rectal Mucosa Donor 31	rectum

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