Variant report

Variant	rs6050308
Chromosome Location	chr20:25064042-25064043
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr20:25061549-25065864	NT2-D1	testis:	n/a	n/a
2	BACH1	chr20:25063965-25064376	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr20:25064000-25064150	GM12870	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25058531..25060558-chr20:25063145..25065745,2	MCF-7	breast:

Variant related genes	Relation type
VSX1	TF binding region
ENSG00000100987	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005409	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[ASN][1000 genomes]
rs2387577	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813546	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815366	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037014	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217195	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217197	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217199	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7263632	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265721	0.80[EUR][1000 genomes]
rs7266451	1.00[ASN][1000 genomes]
rs7344824	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	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	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25061600-25064600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
2	chr20:25061800-25065800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr20:25061800-25065800	Bivalent Enhancer	Fetal Brain Male	brain
4	chr20:25061800-25065800	Enhancers	Pancreas	Pancrea
5	chr20:25062400-25064200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
6	chr20:25062800-25064600	Weak transcription	Gastric	stomach
7	chr20:25063200-25064400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:25063400-25064600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
9	chr20:25063400-25065000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr20:25063600-25064400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr20:25063600-25065400	Bivalent Enhancer	Fetal Heart	heart
12	chr20:25063600-25065800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr20:25063800-25064200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr20:25063800-25064200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr20:25063800-25064200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:25063800-25064200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:25063800-25064200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr20:25063800-25064200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
19	chr20:25063800-25064400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr20:25063800-25064400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr20:25063800-25064400	Bivalent Enhancer	Psoas Muscle	Psoas
22	chr20:25063800-25064400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr20:25063800-25064600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
24	chr20:25063800-25064600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr20:25063800-25064600	Bivalent Enhancer	Fetal Thymus	thymus
26	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr20:25063800-25065200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr20:25063800-25065200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr20:25063800-25065200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:25063800-25065200	Bivalent Enhancer	Liver	Liver
32	chr20:25063800-25065200	Bivalent Enhancer	Esophagus	oesophagus
33	chr20:25063800-25065400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:25063800-25065400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
35	chr20:25063800-25065400	Bivalent Enhancer	Left Ventricle	heart
36	chr20:25063800-25065600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr20:25063800-25065600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
38	chr20:25063800-25065800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
39	chr20:25063800-25065800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr20:25063800-25065800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:25063800-25065800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
42	chr20:25063800-25066000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
43	chr20:25063800-25066400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr20:25064000-25064200	Bivalent Enhancer	Primary T cells from cord blood	blood
45	chr20:25064000-25064200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
46	chr20:25064000-25064200	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
47	chr20:25064000-25064200	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
48	chr20:25064000-25064200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
49	chr20:25064000-25064200	Bivalent Enhancer	Fetal Stomach	stomach
50	chr20:25064000-25064200	Bivalent/Poised TSS	Right Ventricle	heart

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