Variant report

Variant	rs2500428
Chromosome Location	chr20:25275056-25275057
allele	C/G
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25274484..25277309-chr20:25281088..25284844,3	MCF-7	breast:
2	chr20:24975265..24976080-chr20:25274818..25275665,2	MCF-7	breast:
3	chr20:25274762..25275867-chr20:25379505..25380419,5	K562	blood:
4	chr20:25274830..25275740-chr20:25378372..25379283,2	MCF-7	breast:
5	chr20:25274695..25276551-chr20:25281510..25283140,2	K562	blood:
6	chr20:25274862..25275733-chr20:56784800..56785542,2	MCF-7	breast:
7	chr20:25274719..25277448-chr20:25283422..25285264,2	K562	blood:
8	chr20:24999377..25000376-chr20:25274759..25275677,2	K562	blood:
9	chr20:25274847..25275686-chr20:25555235..25555796,2	K562	blood:
10	chr20:25274540..25275681-chr20:25379513..25380502,6	MCF-7	breast:
11	chr20:25268858..25271489-chr20:25274837..25276985,3	K562	blood:
12	chr20:25268242..25271489-chr20:25274837..25277116,3	K562	blood:
13	chr20:25274373..25276866-chr20:25369511..25371754,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 177 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs12106059	1.00[EUR][1000 genomes]
rs12106164	1.00[EUR][1000 genomes]
rs12373881	1.00[EUR][1000 genomes]
rs2039400	1.00[ASN][1000 genomes]
rs2474775	1.00[ASN][1000 genomes]
rs2474776	1.00[ASN][1000 genomes]
rs2482907	1.00[ASN][1000 genomes]
rs2482909	1.00[ASN][1000 genomes]
rs2482917	1.00[ASN][1000 genomes]
rs2482920	1.00[ASN][1000 genomes]
rs2482922	1.00[ASN][1000 genomes]
rs2482925	1.00[ASN][1000 genomes]
rs2482929	1.00[ASN][1000 genomes]
rs2482939	1.00[ASN][1000 genomes]
rs2482942	1.00[ASN][1000 genomes]
rs2482945	1.00[ASN][1000 genomes]
rs2500394	1.00[ASN][1000 genomes]
rs2500396	1.00[ASN][1000 genomes]
rs2500407	1.00[ASN][1000 genomes]
rs2500409	1.00[ASN][1000 genomes]
rs2500412	1.00[ASN][1000 genomes]
rs2500414	1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[ASN][1000 genomes]
rs2500429	1.00[ASN][1000 genomes]
rs2500431	1.00[ASN][1000 genomes]
rs2500434	1.00[ASN][1000 genomes]
rs2500435	1.00[ASN][1000 genomes]
rs2500437	1.00[ASN][1000 genomes]
rs2500438	1.00[ASN][1000 genomes]
rs2500440	1.00[ASN][1000 genomes]
rs2500444	1.00[ASN][1000 genomes]
rs2500445	1.00[ASN][1000 genomes]
rs2500447	1.00[ASN][1000 genomes]
rs28435893	1.00[EUR][1000 genomes]
rs28439563	1.00[EUR][1000 genomes]
rs28551104	1.00[EUR][1000 genomes]
rs2990514	1.00[ASN][1000 genomes]
rs2990515	1.00[ASN][1000 genomes]
rs3002699	1.00[ASN][1000 genomes]
rs3002700	1.00[ASN][1000 genomes]
rs3002703	1.00[ASN][1000 genomes]
rs35073849	1.00[EUR][1000 genomes]
rs364722	1.00[ASN][1000 genomes]
rs368636	1.00[ASN][1000 genomes]
rs380021	1.00[ASN][1000 genomes]
rs384336	1.00[ASN][1000 genomes]
rs426143	1.00[ASN][1000 genomes]
rs428801	1.00[ASN][1000 genomes]
rs429120	1.00[ASN][1000 genomes]
rs432403	1.00[ASN][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs56795563	1.00[EUR][1000 genomes]
rs57237389	1.00[EUR][1000 genomes]
rs57293656	1.00[EUR][1000 genomes]
rs57522322	1.00[EUR][1000 genomes]
rs57579912	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]
rs58957358	1.00[EUR][1000 genomes]
rs59362331	1.00[EUR][1000 genomes]
rs59431257	1.00[EUR][1000 genomes]
rs59857017	1.00[EUR][1000 genomes]
rs6037089	1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	1.00[ASN][1000 genomes]
rs60459445	1.00[EUR][1000 genomes]
rs60479943	1.00[EUR][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050367	1.00[EUR][1000 genomes]
rs6050591	1.00[ASN][1000 genomes]
rs6050613	1.00[ASN][1000 genomes]
rs6050618	1.00[ASN][1000 genomes]
rs6050627	1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs60758360	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]
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]
rs73333142	1.00[EUR][1000 genomes]
rs73333167	1.00[EUR][1000 genomes]
rs73333174	1.00[EUR][1000 genomes]
rs73333187	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[EUR][1000 genomes]
rs73335331	1.00[EUR][1000 genomes]
rs73337199	1.00[EUR][1000 genomes]
rs73339096	1.00[EUR][1000 genomes]
rs73339099	1.00[EUR][1000 genomes]
rs73339100	1.00[EUR][1000 genomes]
rs73341103	1.00[EUR][1000 genomes]
rs73341112	1.00[EUR][1000 genomes]
rs73341114	1.00[EUR][1000 genomes]
rs73341120	1.00[EUR][1000 genomes]
rs73341122	1.00[EUR][1000 genomes]
rs73341124	1.00[EUR][1000 genomes]
rs73341128	1.00[EUR][1000 genomes]
rs73341131	1.00[EUR][1000 genomes]
rs73341135	1.00[EUR][1000 genomes]
rs73341140	1.00[EUR][1000 genomes]
rs73341143	1.00[EUR][1000 genomes]
rs73341155	1.00[EUR][1000 genomes]
rs73341157	1.00[EUR][1000 genomes]
rs73341171	1.00[EUR][1000 genomes]
rs73343010	1.00[EUR][1000 genomes]
rs73343043	1.00[EUR][1000 genomes]
rs73343050	1.00[EUR][1000 genomes]
rs73343053	1.00[EUR][1000 genomes]
rs73343058	1.00[EUR][1000 genomes]
rs73343090	1.00[EUR][1000 genomes]
rs73343097	1.00[EUR][1000 genomes]
rs73345003	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]
rs73904476	1.00[ASN][1000 genomes]
rs73907308	1.00[ASN][1000 genomes]
rs73907312	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]
rs8115188	1.00[EUR][1000 genomes]
rs8118017	1.00[EUR][1000 genomes]
rs8119273	1.00[EUR][1000 genomes]
rs8120601	1.00[EUR][1000 genomes]
rs8121557	1.00[EUR][1000 genomes]
rs9967947	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	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
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
18	nsv912827	chr20:25271326-25288632	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:25249200-25285800	Strong transcription	Dnd41	blood
6	chr20:25249400-25276200	Strong transcription	Fetal Intestine Large	intestine
7	chr20:25249600-25275200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr20:25249800-25275200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr20:25249800-25275200	Strong transcription	Fetal Stomach	stomach
14	chr20:25249800-25276400	Strong transcription	Fetal Intestine Small	intestine
15	chr20:25249800-25284400	Strong transcription	Brain Germinal Matrix	brain
16	chr20:25250000-25275800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:25250600-25276200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:25250800-25285000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:25251400-25275400	Strong transcription	Thymus	Thymus
20	chr20:25252200-25276400	Weak transcription	Hela-S3	cervix
21	chr20:25254000-25276200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr20:25254400-25287800	Weak transcription	K562	blood
23	chr20:25255600-25279200	Strong transcription	Fetal Brain Female	brain
24	chr20:25255800-25290000	Weak transcription	Small Intestine	intestine
25	chr20:25256000-25299400	Weak transcription	Fetal Brain Male	brain
26	chr20:25259000-25275600	Weak transcription	Right Atrium	heart
27	chr20:25259000-25290800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr20:25260000-25275400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr20:25261600-25291000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr20:25265000-25275800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr20:25266600-25291200	Weak transcription	Primary B cells from cord blood	blood
32	chr20:25267000-25291200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr20:25267600-25276400	Weak transcription	HUVEC	blood vessel
34	chr20:25267600-25279200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr20:25269200-25281600	Weak transcription	Liver	Liver
36	chr20:25270400-25278800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr20:25270800-25277200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr20:25271400-25279600	Genic enhancers	HMEC	breast
39	chr20:25271400-25290600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr20:25271600-25291200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:25271800-25276800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr20:25272200-25275400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr20:25272200-25276400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr20:25272400-25275800	Weak transcription	NHDF-Ad	bronchial
45	chr20:25272400-25277000	Weak transcription	Ovary	ovary
46	chr20:25272400-25277600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr20:25272600-25275400	Weak transcription	Brain Substantia Nigra	brain
48	chr20:25272600-25277000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr20:25272800-25275200	Weak transcription	HSMM	muscle
50	chr20:25272800-25276200	Weak transcription	Fetal Lung	lung

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