Variant report

Variant	rs28733778
Chromosome Location	chr20:25482779-25482780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25480268..25483016-chr20:25564719..25567825,3	MCF-7	breast:
2	chr20:25481164..25483105-chr20:25484955..25487000,2	K562	blood:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs28417591	1.00[EUR][1000 genomes]
rs28439563	1.00[EUR][1000 genomes]
rs28551104	1.00[EUR][1000 genomes]
rs417446	1.00[EUR][1000 genomes]
rs56795563	1.00[EUR][1000 genomes]
rs57237389	1.00[EUR][1000 genomes]
rs57522322	1.00[EUR][1000 genomes]
rs57579912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58189090	1.00[EUR][1000 genomes]
rs58410604	1.00[EUR][1000 genomes]
rs58593226	1.00[EUR][1000 genomes]
rs58709664	1.00[EUR][1000 genomes]
rs58722006	1.00[EUR][1000 genomes]
rs59362331	1.00[EUR][1000 genomes]
rs59431257	1.00[EUR][1000 genomes]
rs59826126	1.00[EUR][1000 genomes]
rs60459445	1.00[EUR][1000 genomes]
rs60758360	1.00[EUR][1000 genomes]
rs60772859	1.00[EUR][1000 genomes]
rs60831246	1.00[EUR][1000 genomes]
rs60834749	1.00[EUR][1000 genomes]
rs60893899	1.00[EUR][1000 genomes]
rs7264066	1.00[EUR][1000 genomes]
rs7267807	1.00[EUR][1000 genomes]
rs7274976	1.00[EUR][1000 genomes]
rs73331819	1.00[EUR][1000 genomes]
rs73331822	1.00[EUR][1000 genomes]
rs73331824	1.00[EUR][1000 genomes]
rs73331833	1.00[EUR][1000 genomes]
rs73331834	1.00[EUR][1000 genomes]
rs73331856	1.00[EUR][1000 genomes]
rs73331880	1.00[EUR][1000 genomes]
rs73331881	1.00[EUR][1000 genomes]
rs73333506	1.00[EUR][1000 genomes]
rs73333515	1.00[EUR][1000 genomes]
rs73333541	1.00[EUR][1000 genomes]
rs73333553	1.00[EUR][1000 genomes]
rs73333566	1.00[EUR][1000 genomes]
rs73333583	1.00[EUR][1000 genomes]
rs73333590	1.00[EUR][1000 genomes]
rs73335304	1.00[EUR][1000 genomes]
rs73335318	1.00[EUR][1000 genomes]
rs73335329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335348	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335353	1.00[EUR][1000 genomes]
rs73335363	1.00[EUR][1000 genomes]
rs73335366	1.00[EUR][1000 genomes]
rs73335375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73335383	1.00[EUR][1000 genomes]
rs73335389	1.00[EUR][1000 genomes]
rs73335394	1.00[EUR][1000 genomes]
rs73335398	1.00[EUR][1000 genomes]
rs73335400	1.00[EUR][1000 genomes]
rs73335402	1.00[EUR][1000 genomes]
rs73337303	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337317	1.00[EUR][1000 genomes]
rs73337328	1.00[EUR][1000 genomes]
rs73337350	1.00[AMR][1000 genomes]
rs73337360	1.00[EUR][1000 genomes]
rs73337362	1.00[EUR][1000 genomes]
rs73337380	1.00[EUR][1000 genomes]
rs73337391	1.00[EUR][1000 genomes]
rs73339340	1.00[EUR][1000 genomes]
rs73339342	1.00[EUR][1000 genomes]
rs73339354	1.00[EUR][1000 genomes]
rs73339363	1.00[EUR][1000 genomes]
rs73339381	1.00[EUR][1000 genomes]
rs73345011	1.00[EUR][1000 genomes]
rs73345016	1.00[EUR][1000 genomes]
rs73345021	1.00[EUR][1000 genomes]
rs73345030	1.00[EUR][1000 genomes]
rs73345040	1.00[EUR][1000 genomes]
rs73345068	1.00[EUR][1000 genomes]
rs73345069	1.00[EUR][1000 genomes]
rs73345071	1.00[EUR][1000 genomes]
rs73345073	1.00[EUR][1000 genomes]
rs73345082	1.00[EUR][1000 genomes]
rs73345087	1.00[EUR][1000 genomes]
rs73345088	1.00[EUR][1000 genomes]
rs73347023	1.00[EUR][1000 genomes]
rs73347042	1.00[EUR][1000 genomes]
rs73347058	1.00[EUR][1000 genomes]
rs8118017	1.00[EUR][1000 genomes]
rs9941767	1.00[EUR][1000 genomes]
rs9967947	1.00[EUR][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	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
2	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
3	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
6	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr20:25451400-25488800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
10	chr20:25457800-25489000	Weak transcription	Placenta	Placenta
11	chr20:25459800-25489800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr20:25462800-25488200	Weak transcription	Colonic Mucosa	Colon
13	chr20:25465000-25483000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr20:25465600-25490000	Weak transcription	Brain Angular Gyrus	brain
15	chr20:25465800-25488000	Weak transcription	Fetal Kidney	kidney
16	chr20:25466000-25484200	Weak transcription	Fetal Brain Male	brain
17	chr20:25467400-25484200	Weak transcription	Left Ventricle	heart
18	chr20:25467400-25491800	Weak transcription	Primary T cells from cord blood	blood
19	chr20:25467600-25488000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr20:25468600-25484200	Weak transcription	HUVEC	blood vessel
21	chr20:25469800-25484200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr20:25470000-25483000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr20:25470000-25488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:25470000-25488000	Weak transcription	Osteobl	bone
25	chr20:25470200-25484200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:25470600-25484200	Weak transcription	NHLF	lung
27	chr20:25470800-25484200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr20:25470800-25484400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr20:25471000-25488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr20:25471400-25483000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:25472000-25483600	Weak transcription	Lung	lung
32	chr20:25472000-25484200	Weak transcription	Adipose Nuclei	Adipose
33	chr20:25472400-25483200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr20:25472400-25484200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr20:25473200-25487800	Weak transcription	Fetal Heart	heart
36	chr20:25473400-25484400	Strong transcription	Ovary	ovary
37	chr20:25473400-25494400	Strong transcription	Fetal Brain Female	brain
38	chr20:25473600-25494600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr20:25473600-25494600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr20:25473800-25485800	Strong transcription	Fetal Intestine Small	intestine
41	chr20:25473800-25494200	Strong transcription	Thymus	Thymus
42	chr20:25474400-25495200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr20:25474600-25484400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr20:25474600-25494800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr20:25474800-25493400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr20:25475400-25494000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25475400-25498000	Weak transcription	Right Ventricle	heart
48	chr20:25477000-25494800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr20:25477400-25495200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr20:25478000-25488000	Weak transcription	NH-A	brain

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