Variant report

Variant	rs56369722
Chromosome Location	chr20:25064491-25064492
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:87)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:87 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:25064400-25064550	HCT-116	colon:	n/a	n/a
2	CTCF	chr20:25064360-25064510	GM12865	blood:	n/a	n/a
3	CTCF	chr20:25064440-25064590	GM12864	blood:	n/a	n/a
4	CTCF	chr20:25064380-25064530	HVMF	connective:	n/a	n/a
5	CTCF	chr20:25064254-25064660	MCF-7	breast:	n/a	n/a
6	CTCF	chr20:25064378-25064591	Pancreas_OC	pancreas:	n/a	n/a
7	CTCF	chr20:25064380-25064530	HAc	cerebellar:	n/a	n/a
8	CTCF	chr20:25064420-25064570	AG04450	lung:	n/a	n/a
9	CTCF	chr20:25064396-25064566	GM13977	blood:	n/a	n/a
10	CTCF	chr20:25064324-25064685	MCF-7	breast:	n/a	n/a
11	CTCF	chr20:25064422-25064533	Spleen_OC	spleen:	n/a	n/a
12	CTCF	chr20:25064440-25064590	GM12874	blood:	n/a	n/a
13	CTCF	chr20:25064400-25064550	AG04449	skin:	n/a	n/a
14	SUZ12	chr20:25061549-25065864	NT2-D1	testis:	n/a	n/a
15	CTCF	chr20:25064385-25064621	MCF-7	breast:	n/a	n/a
16	CTCF	chr20:25064420-25064570	HPF	lung:	n/a	n/a
17	CTCF	chr20:25064380-25064530	GM12865	blood:	n/a	n/a
18	CTCF	chr20:25064440-25064590	GM12875	blood:	n/a	n/a
19	CTCF	chr20:25064374-25064609	GM19238	blood:	n/a	n/a
20	CTCF	chr20:25064400-25064550	HUVEC	blood vessel:	n/a	n/a
21	CTCF	chr20:25064400-25064550	HFF-Myc	foreskin:	n/a	n/a
22	CTCF	chr20:25064380-25064530	GM12875	blood:	n/a	n/a
23	CTCF	chr20:25064430-25064567	Lung_OC	lung:	n/a	n/a
24	CTCF	chr20:25064440-25064590	HUVEC	blood vessel:	n/a	n/a
25	CTCF	chr20:25064480-25064630	HCT-116	colon:	n/a	n/a
26	CTCF	chr20:25064420-25064570	GM12867	blood:	n/a	n/a
27	CTCF	chr20:25064360-25064510	AG10803	skin:	n/a	n/a
28	CTCF	chr20:25064420-25064570	WERI-Rb-1	eye:	n/a	n/a
29	CTCF	chr20:25064380-25064530	BJ	skin:	n/a	n/a
30	CTCF	chr20:25064400-25064550	HCPEpiC	choroid plexus:	n/a	n/a
31	CTCF	chr20:25064400-25064550	GM12871	blood:	n/a	n/a
32	CTCF	chr20:25064392-25064599	MCF-7	breast:	n/a	n/a
33	CTCF	chr20:25064380-25064530	GM12870	blood:	n/a	n/a
34	CTCF	chr20:25064400-25064550	BJ	skin:	n/a	n/a
35	CTCF	chr20:25064358-25064633	NHEK	skin:	n/a	n/a
36	CTCF	chr20:25064420-25064570	GM12869	blood:	n/a	n/a
37	CTCF	chr20:25064388-25064589	MCF-7	breast:	n/a	n/a
38	CTCF	chr20:25064400-25064550	AG10803	skin:	n/a	n/a
39	CTCF	chr20:25064363-25064631	GM19240	blood:	n/a	n/a
40	CTCF	chr20:25064400-25064550	GM12870	blood:	n/a	n/a
41	RAD21	chr20:25064228-25064632	MCF-7	breast:	n/a	n/a
42	CTCF	chr20:25064388-25064591	MCF-7	breast:	n/a	n/a
43	CTCF	chr20:25064360-25064510	GM12872	blood:	n/a	n/a
44	CTCF	chr20:25064380-25064530	BE2_C	brain:	n/a	n/a
45	CTCF	chr20:25064400-25064550	GM12869	blood:	n/a	n/a
46	RAD21	chr20:25064188-25064739	HCT-116	colon:	n/a	n/a
47	CTCF	chr20:25064460-25064610	HRE	kidney:	n/a	n/a
48	CTCF	chr20:25064440-25064590	RPTEC	kidney:	n/a	n/a
49	CTCF	chr20:25064380-25064530	HRPEpiC	eye:	n/a	n/a
50	CTCF	chr20:25064389-25064582	GM19239	blood:	n/a	n/a

No data

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

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

No data

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	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[ASN][1000 genomes]
rs2387577	1.00[ASN][1000 genomes]
rs4813546	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815366	1.00[ASN][1000 genomes]
rs4815367	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037014	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	0.89[AFR][1000 genomes];0.96[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	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083737	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	0.89[AFR][1000 genomes];0.99[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	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217195	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.85[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	0.87[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	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.96[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:74 , 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	chr20:25062800-25064600	Weak transcription	Gastric	stomach
6	chr20:25063400-25064600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
7	chr20:25063400-25065000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr20:25063600-25065400	Bivalent Enhancer	Fetal Heart	heart
9	chr20:25063600-25065800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr20:25063800-25064600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
11	chr20:25063800-25064600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr20:25063800-25064600	Bivalent Enhancer	Fetal Thymus	thymus
13	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr20:25063800-25065200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
16	chr20:25063800-25065200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:25063800-25065200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr20:25063800-25065200	Bivalent Enhancer	Liver	Liver
19	chr20:25063800-25065200	Bivalent Enhancer	Esophagus	oesophagus
20	chr20:25063800-25065400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:25063800-25065400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr20:25063800-25065400	Bivalent Enhancer	Left Ventricle	heart
23	chr20:25063800-25065600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:25063800-25065600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
25	chr20:25063800-25065800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
26	chr20:25063800-25065800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr20:25063800-25065800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr20:25063800-25065800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
29	chr20:25063800-25066000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
30	chr20:25063800-25066400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr20:25064000-25064600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr20:25064000-25064600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr20:25064000-25064600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr20:25064000-25064800	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:25064000-25064800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:25064000-25064800	Bivalent/Poised TSS	Thymus	Thymus
37	chr20:25064000-25065000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
38	chr20:25064000-25065000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr20:25064000-25065000	Bivalent Enhancer	Stomach Mucosa	stomach
40	chr20:25064000-25065200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
41	chr20:25064000-25065400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr20:25064000-25065400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
43	chr20:25064000-25065600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
44	chr20:25064000-25065600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
45	chr20:25064000-25065600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
46	chr20:25064000-25065800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
47	chr20:25064000-25065800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr20:25064000-25065800	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr20:25064000-25066000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr20:25064200-25064600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links