Variant report

Variant	rs6115024
Chromosome Location	chr20:25064312-25064313
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:25064254-25064660	MCF-7	breast:	n/a	n/a
2	SUZ12	chr20:25061549-25065864	NT2-D1	testis:	n/a	n/a
3	BACH1	chr20:25063965-25064376	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr20:25064228-25064632	MCF-7	breast:	n/a	n/a
5	RAD21	chr20:25064188-25064739	HCT-116	colon:	n/a	n/a
6	SUZ12	chr20:25064083-25065434	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr20:25064215-25064725	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:25064268-25064318	HMEC	breast:	n/a
2	chr20:25064268-25064318	K562	blood:	n/a
3	chr20:25064268-25064318	SK-N-SH_RA	brain:	n/a
4	chr20:25064268-25064318	U87	brain:	n/a
5	chr20:25064268-25064318	HCPEpiC	choroid plexus:	n/a
6	chr20:25064268-25064318	SAEC	small airway:	n/a
7	chr20:25064268-25064318	CMK	blood:	n/a
8	chr20:25064268-25064318	HepG2	liver:	n/a
9	chr20:25064268-25064318	AG09319	gingival:	n/a
10	chr20:25064268-25064318	SKMC	muscle:	n/a
11	chr20:25064268-25064318	MCF10A-Er-Src	breast:	n/a
12	chr20:25064268-25064318	A549	lung:	n/a
13	chr20:25064268-25064318	Hela-S3	cervix:	n/a
14	chr20:25064268-25064318	AG04449	skin:	fetal
15	chr20:25064268-25064318	T-47D	breast:	n/a
16	chr20:25064268-25064318	AG04450	lung:	fetal
17	chr20:25064268-25064318	HIPEpiC	eye:	n/a
18	chr20:25064268-25064318	ProgFib	skin:	n/a
19	chr20:25064268-25064318	GM19239	blood:	n/a
20	chr20:25064268-25064318	AG09309	skin:	n/a
21	chr20:25064268-25064318	IMR90	lung:	fetal
22	chr20:25064268-25064318	HNPCEpiC	eye:	n/a
23	chr20:25064268-25064318	HUVEC	blood vessel:	n/a
24	chr20:25064268-25064318	NH-A	brain:	n/a
25	chr20:25064268-25064318	BE2_C	brain:	n/a
26	chr20:25064268-25064318	HL-60	blood:	n/a
27	chr20:25064268-25064318	SK-N-MC	brain:	n/a
28	chr20:25064268-25064318	RPTEC	kidney:	n/a
29	chr20:25064268-25064318	BJ	skin:	n/a
30	chr20:25064268-25064318	SK-N-SH	brain:	n/a
31	chr20:25064268-25064318	GM12892	blood:	n/a
32	chr20:25064268-25064318	AoSMC	blood vessel:	n/a
33	chr20:25064268-25064318	HEEpiC	esophagus:	n/a
34	chr20:25064268-25064318	HRPEpiC	eye:	n/a
35	chr20:25064268-25064318	ovcar-3	ovarian:	n/a
36	chr20:25064268-25064318	PANC-1	pancreas:	n/a
37	chr20:25064268-25064318	PrEC	prostate:	n/a
38	chr20:25064268-25064318	H1-hESC	embryonic stem cell:	embryo
39	chr20:25064268-25064318	HEK293	kidney:	embryo
40	chr20:25064268-25064318	ECC-1	luminal epithelium:	n/a
41	chr20:25064268-25064318	GM12891	blood:	n/a
42	chr20:25064268-25064318	AG10803	skin:	n/a
43	chr20:25064268-25064318	NHBE	bronchial:	n/a
44	chr20:25064268-25064318	HRE	kidney:	n/a
45	chr20:25064268-25064318	PFSK-1	brain:	n/a
46	chr20:25064268-25064318	HRCEpiC	kidney:	n/a
47	chr20:25064268-25064318	MCF-7	breast:	n/a
48	chr20:25064268-25064318	LNCaP	prostate:	n/a
49	chr20:25064268-25064318	HCF	heart:	n/a
50	chr20:25064268-25064318	GM06990	blood:	n/a

(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
VSX1	CpG island
ENSG00000100987	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1005409	1.00[ASN][1000 genomes]
rs12480307	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs2144372	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2207632	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs2207633	1.00[ASN][1000 genomes]
rs2207635	1.00[ASN][1000 genomes]
rs2207636	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2387577	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892313	0.89[AFR][1000 genomes]
rs4813546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4813548	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815364	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs4815366	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4815368	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs55651034	1.00[ASN][1000 genomes]
rs56157240	1.00[ASN][1000 genomes]
rs56369722	1.00[ASN][1000 genomes]
rs58747756	1.00[ASN][1000 genomes]
rs6037013	1.00[JPT][hapmap]
rs6037014	1.00[ASN][1000 genomes]
rs6050299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6050300	1.00[ASN][1000 genomes]
rs6050304	1.00[ASN][1000 genomes]
rs6050306	1.00[ASN][1000 genomes]
rs6050308	1.00[ASN][1000 genomes]
rs6076315	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6083734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	1.00[ASN][1000 genomes]
rs6083737	1.00[ASN][1000 genomes]
rs6083739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs6083745	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6115026	0.91[AFR][1000 genomes]
rs6115037	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61304082	1.00[ASN][1000 genomes]
rs62215277	1.00[ASN][1000 genomes]
rs62217195	1.00[ASN][1000 genomes]
rs62217196	1.00[ASN][1000 genomes]
rs62217197	1.00[ASN][1000 genomes]
rs62217199	1.00[ASN][1000 genomes]
rs7263632	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7266451	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7344824	1.00[ASN][1000 genomes]
rs743017	1.00[ASN][1000 genomes]
rs743018	0.94[ASW][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6115024	VSX1	cis	cerebellum	SCAN
rs6115024	C20orf3	cis	cerebellum	SCAN
rs6115024	ACSS1	cis	cerebellum	SCAN

Chromatin state (count:80 , 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	chr20:25063200-25064400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr20:25063400-25064600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
8	chr20:25063400-25065000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr20:25063600-25064400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr20:25063600-25065400	Bivalent Enhancer	Fetal Heart	heart
11	chr20:25063600-25065800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr20:25063800-25064400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:25063800-25064400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:25063800-25064400	Bivalent Enhancer	Psoas Muscle	Psoas
15	chr20:25063800-25064400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
16	chr20:25063800-25064600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
17	chr20:25063800-25064600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:25063800-25064600	Bivalent Enhancer	Fetal Thymus	thymus
19	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr20:25063800-25065200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
22	chr20:25063800-25065200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr20:25063800-25065200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr20:25063800-25065200	Bivalent Enhancer	Liver	Liver
25	chr20:25063800-25065200	Bivalent Enhancer	Esophagus	oesophagus
26	chr20:25063800-25065400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr20:25063800-25065400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
28	chr20:25063800-25065400	Bivalent Enhancer	Left Ventricle	heart
29	chr20:25063800-25065600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr20:25063800-25065600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
31	chr20:25063800-25065800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
32	chr20:25063800-25065800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr20:25063800-25065800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr20:25063800-25065800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
35	chr20:25063800-25066000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
36	chr20:25063800-25066400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr20:25064000-25064400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:25064000-25064400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr20:25064000-25064400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr20:25064000-25064400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
41	chr20:25064000-25064400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
42	chr20:25064000-25064400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
43	chr20:25064000-25064400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
44	chr20:25064000-25064400	Bivalent Enhancer	NH-A	brain
45	chr20:25064000-25064400	Bivalent/Poised TSS	NHEK	skin
46	chr20:25064000-25064600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr20:25064000-25064600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr20:25064000-25064600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:25064000-25064800	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr20:25064000-25064800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain

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