Variant report

Variant	rs6050490
Chromosome Location	chr20:25238235-25238236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25232688..25236951-chr20:25237254..25241133,6	K562	blood:
2	chr20:25183731..25186136-chr20:25238166..25239977,2	MCF-7	breast:
3	chr20:25233973..25236951-chr20:25237621..25241133,4	K562	blood:
4	chr20:25175397..25177963-chr20:25237713..25239938,2	MCF-7	breast:
5	chr20:25237526..25240142-chr20:25247989..25249808,2	K562	blood:

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11907515	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2067793	1.00[EUR][1000 genomes]
rs2145125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2228978	1.00[EUR][1000 genomes]
rs2387734	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28496800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28770021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28881233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34299454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41282340	1.00[EUR][1000 genomes]
rs41304802	1.00[EUR][1000 genomes]
rs41308633	1.00[EUR][1000 genomes]
rs58412968	0.83[EUR][1000 genomes]
rs58953621	0.83[EUR][1000 genomes]
rs59082275	0.83[EUR][1000 genomes]
rs6037061	1.00[EUR][1000 genomes]
rs6037064	1.00[EUR][1000 genomes]
rs6037068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037070	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050449	1.00[EUR][1000 genomes]
rs6050451	1.00[EUR][1000 genomes]
rs6050457	1.00[EUR][1000 genomes]
rs6050458	1.00[EUR][1000 genomes]
rs6050461	1.00[EUR][1000 genomes]
rs6050462	1.00[EUR][1000 genomes]
rs6050465	1.00[EUR][1000 genomes]
rs6050473	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050474	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050476	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050478	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050485	0.83[AFR][1000 genomes]
rs6050486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050495	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050505	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050507	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050509	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050512	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7263527	1.00[EUR][1000 genomes]
rs7269045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7273544	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7274919	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73343076	0.83[EUR][1000 genomes]
rs73347016	0.83[EUR][1000 genomes]
rs73347066	0.83[EUR][1000 genomes]
rs7344105	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs736358	1.00[EUR][1000 genomes]
rs8116564	1.00[EUR][1000 genomes]
rs8118763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8120268	1.00[EUR][1000 genomes]
rs8123947	0.83[EUR][1000 genomes]
rs8125980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];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	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25229800-25250000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:25230200-25239000	Weak transcription	Primary B cells from cord blood	blood
3	chr20:25230200-25239600	Enhancers	Stomach Mucosa	stomach
4	chr20:25230200-25239800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr20:25230200-25240400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr20:25230200-25240400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr20:25230400-25239800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr20:25230400-25239800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr20:25230600-25239800	Weak transcription	Fetal Lung	lung
11	chr20:25231000-25239400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:25231000-25239800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr20:25231000-25240400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr20:25231200-25239200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr20:25231200-25251800	Weak transcription	Hela-S3	cervix
16	chr20:25231200-25252200	Weak transcription	HUVEC	blood vessel
17	chr20:25231400-25240000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr20:25231400-25240800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr20:25231400-25249800	Weak transcription	Small Intestine	intestine
20	chr20:25232000-25239400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr20:25232000-25239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr20:25232600-25238600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:25232600-25240000	Weak transcription	Thymus	Thymus
24	chr20:25233200-25238400	Weak transcription	K562	blood
25	chr20:25233200-25239200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:25233200-25239400	Enhancers	Primary T cells from cord blood	blood
27	chr20:25233200-25252200	Weak transcription	Fetal Brain Male	brain
28	chr20:25234000-25239200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr20:25234000-25239200	Weak transcription	Spleen	Spleen
30	chr20:25234000-25240000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr20:25234000-25240200	Weak transcription	HSMM	muscle
32	chr20:25234600-25238400	Enhancers	Adipose Nuclei	Adipose
33	chr20:25234600-25242400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr20:25235000-25239600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr20:25235000-25243000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr20:25235600-25239800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
38	chr20:25235800-25240000	Weak transcription	Fetal Brain Female	brain
39	chr20:25236000-25238600	Enhancers	Brain Anterior Caudate	brain
40	chr20:25236000-25238800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr20:25236000-25239200	Strong transcription	Fetal Stomach	stomach
42	chr20:25236000-25239800	Weak transcription	NH-A	brain
43	chr20:25236000-25242200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr20:25236200-25238400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr20:25236200-25238600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr20:25236200-25238600	Enhancers	Fetal Heart	heart
47	chr20:25236200-25238800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr20:25236200-25238800	Weak transcription	Brain Germinal Matrix	brain
49	chr20:25236200-25239000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr20:25236200-25239200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links