Variant report

Variant	rs28469564
Chromosome Location	chr19:42791462-42791463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
2	chr19:42786948..42794333-chr19:42803465..42809501,23	K562	blood:
3	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188368	Chromatin interaction
ENSG00000204957	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000268643	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10401224	1.00[EUR][1000 genomes]
rs10402438	1.00[EUR][1000 genomes]
rs10404650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406800	1.00[AMR][1000 genomes]
rs10406972	1.00[EUR][1000 genomes]
rs10407085	1.00[EUR][1000 genomes]
rs10407155	1.00[EUR][1000 genomes]
rs10407842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408141	0.89[AFR][1000 genomes]
rs10408258	1.00[EUR][1000 genomes]
rs10409428	1.00[EUR][1000 genomes]
rs10409433	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409939	1.00[EUR][1000 genomes]
rs10410129	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410174	1.00[AMR][1000 genomes]
rs10410653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411498	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411908	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415478	0.81[AFR][1000 genomes]
rs10415759	1.00[AMR][1000 genomes]
rs10415999	1.00[EUR][1000 genomes]
rs10416535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421331	1.00[AMR][1000 genomes]
rs10421409	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421510	1.00[EUR][1000 genomes]
rs10421857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421902	1.00[AMR][1000 genomes]
rs10422301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422867	1.00[EUR][1000 genomes]
rs10423812	1.00[EUR][1000 genomes]
rs10423959	1.00[EUR][1000 genomes]
rs10423978	1.00[EUR][1000 genomes]
rs10424402	1.00[EUR][1000 genomes]
rs10425003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425320	1.00[EUR][1000 genomes]
rs10425783	1.00[EUR][1000 genomes]
rs10426267	1.00[EUR][1000 genomes]
rs10426284	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878297	1.00[EUR][1000 genomes]
rs11879073	1.00[EUR][1000 genomes]
rs11879538	1.00[EUR][1000 genomes]
rs11880214	1.00[EUR][1000 genomes]
rs11880356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882107	1.00[EUR][1000 genomes]
rs11882801	1.00[EUR][1000 genomes]
rs12165130	1.00[EUR][1000 genomes]
rs13343322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13346837	1.00[EUR][1000 genomes]
rs2229614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28463673	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28474957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28483598	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28496975	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28657829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28675019	1.00[EUR][1000 genomes]
rs28675764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28699037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28711448	1.00[EUR][1000 genomes]
rs28715574	1.00[EUR][1000 genomes]
rs33919763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35707383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36089262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41407146	1.00[AMR][1000 genomes]
rs59870753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60950516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7254853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7255343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258727	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73552879	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73554520	1.00[EUR][1000 genomes]
rs73554531	1.00[EUR][1000 genomes]
rs73558432	1.00[AMR][1000 genomes]
rs8099885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9304602	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
8	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
9	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
10	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
11	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
12	nsv911787	chr19:42773862-42795554	Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42788800-42792400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:42789800-42791600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:42790000-42793400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:42790200-42795400	Weak transcription	Hela-S3	cervix
5	chr19:42790200-42800200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:42790400-42792200	Genic enhancers	Right Ventricle	heart
7	chr19:42790400-42794800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:42790600-42791600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:42790600-42791800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:42790600-42792000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr19:42790600-42792200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:42790600-42792200	Weak transcription	Small Intestine	intestine
13	chr19:42790600-42793800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:42790600-42794000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:42790600-42797800	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr19:42790600-42801600	Strong transcription	Dnd41	blood
17	chr19:42790600-42802400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:42790600-42804600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:42790600-42804800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:42790600-42805000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:42790600-42805400	Weak transcription	Stomach Mucosa	stomach
22	chr19:42790600-42806000	Weak transcription	Psoas Muscle	Psoas
23	chr19:42790800-42791600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr19:42790800-42791600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr19:42790800-42792000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr19:42790800-42794200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:42790800-42794400	Strong transcription	A549	lung
28	chr19:42790800-42794600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:42790800-42799000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:42790800-42802000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:42790800-42802200	Strong transcription	Thymus	Thymus
32	chr19:42791000-42792000	Genic enhancers	Pancreas	Pancrea
33	chr19:42791000-42792600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr19:42791000-42794000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr19:42791000-42794000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:42791000-42795000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:42791000-42795000	Strong transcription	Fetal Thymus	thymus
38	chr19:42791000-42795200	Strong transcription	NHEK	skin
39	chr19:42791000-42795800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr19:42791000-42796000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:42791000-42799200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:42791000-42799600	Strong transcription	HSMMtube	muscle
43	chr19:42791000-42799800	Strong transcription	Lung	lung
44	chr19:42791000-42800200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:42791000-42800200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:42791000-42801400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:42791000-42801600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr19:42791000-42801600	Strong transcription	NHLF	lung
49	chr19:42791000-42802800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:42791200-42791600	Genic enhancers	Primary monocytes fromperipheralblood	blood

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