Variant report

Variant	rs6097627
Chromosome Location	chr20:52457873-52457874
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:70148331..70150466-chr20:52456396..52458617,2	MCF-7	breast:
2	chr20:52457397..52459332-chr3:62860630..62862547,2	MCF-7	breast:
3	chr20:52457233..52457942-chr4:55449043..55449853,2	MCF-7	breast:
4	chr20:52455663..52458624-chr20:52464778..52466415,2	K562	blood:

Variant related genes	Relation type
ENSG00000127328	Chromatin interaction
ENSG00000163618	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs6091757	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6091760	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097619	0.81[AFR][1000 genomes]
rs6097620	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097621	0.96[AFR][1000 genomes]
rs6097622	0.92[AFR][1000 genomes]
rs6097623	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097633	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097634	0.85[AFR][1000 genomes]
rs7261242	0.96[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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52447400-52459400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr20:52449800-52461000	Enhancers	Primary B cells from peripheral blood	blood
3	chr20:52450000-52462000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr20:52450400-52465200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr20:52450600-52465200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr20:52451000-52462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:52451200-52464000	Weak transcription	HSMM	muscle
8	chr20:52452400-52463800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr20:52452400-52465200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr20:52452600-52461400	Weak transcription	Osteobl	bone
11	chr20:52453600-52458000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr20:52453600-52480200	Weak transcription	Small Intestine	intestine
13	chr20:52454400-52464200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr20:52455000-52459000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr20:52455000-52464800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr20:52456400-52458000	Enhancers	GM12878-XiMat	blood
17	chr20:52456400-52463200	Weak transcription	Spleen	Spleen
18	chr20:52456600-52459000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr20:52456600-52459200	Weak transcription	Thymus	Thymus
20	chr20:52456600-52463800	Weak transcription	Fetal Lung	lung
21	chr20:52456600-52468400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr20:52456600-52476200	Weak transcription	Gastric	stomach
23	chr20:52456800-52459200	Weak transcription	Fetal Intestine Large	intestine
24	chr20:52456800-52459200	Weak transcription	Fetal Intestine Small	intestine
25	chr20:52457000-52458400	Weak transcription	Fetal Thymus	thymus
26	chr20:52457000-52458800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr20:52457000-52459000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr20:52457000-52459200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr20:52457000-52459200	Weak transcription	Colonic Mucosa	Colon
30	chr20:52457000-52462400	Weak transcription	HepG2	liver
31	chr20:52457200-52458400	Weak transcription	Dnd41	blood
32	chr20:52457200-52459000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr20:52457200-52459000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr20:52457200-52459200	Weak transcription	Stomach Mucosa	stomach
35	chr20:52457400-52458600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr20:52457400-52458800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr20:52457400-52458800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr20:52457400-52459000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr20:52457400-52459200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr20:52457400-52459200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr20:52457400-52461000	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr20:52457600-52458600	Weak transcription	Primary T cells from cord blood	blood
43	chr20:52457600-52458800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr20:52457600-52459000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr20:52457600-52459000	Weak transcription	NHEK	skin
46	chr20:52457600-52461400	Weak transcription	NHDF-Ad	bronchial
47	chr20:52457600-52462600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr20:52457800-52458200	Weak transcription	Primary B cells from cord blood	blood
49	chr20:52457800-52458800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr20:52457800-52458800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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