Variant report

Variant	rs56374952
Chromosome Location	chr20:25130596-25130597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr20:25130529-25130760	HepG2	liver:	n/a	n/a
2	MAFF	chr20:25130523-25130718	HepG2	liver:	n/a	n/a
3	MAFK	chr20:25130463-25130682	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:25130549-25130599	GM06990	blood:	n/a
2	chr20:25130549-25130599	HAEpiC	amniotic membrane:	n/a
3	chr20:25130549-25130599	GM12878	blood:	n/a
4	chr20:25130549-25130599	U87	brain:	n/a
5	chr20:25130549-25130599	H1-hESC	embryonic stem cell:	embryo
6	chr20:25130549-25130599	ProgFib	skin:	n/a
7	chr20:25130549-25130599	NHDF-neo	bronchial:	n/a
8	chr20:25130549-25130599	AG09319	gingival:	n/a
9	chr20:25130549-25130599	BJ	skin:	n/a
10	chr20:25130549-25130599	HUVEC	blood vessel:	n/a
11	chr20:25130549-25130599	Jurkat	blood:	n/a
12	chr20:25130549-25130599	IMR90	lung:	fetal
13	chr20:25130549-25130599	AG04450	lung:	fetal
14	chr20:25130549-25130599	NHBE	bronchial:	n/a
15	chr20:25130549-25130599	HRPEpiC	eye:	n/a
16	chr20:25130549-25130599	ovcar-3	ovarian:	n/a
17	chr20:25130549-25130599	CMK	blood:	n/a
18	chr20:25130549-25130599	GM12891	blood:	n/a
19	chr20:25130549-25130599	HCM	heart:	n/a
20	chr20:25130549-25130599	SKMC	muscle:	n/a
21	chr20:25130549-25130599	HCPEpiC	choroid plexus:	n/a
22	chr20:25130549-25130599	BE2_C	brain:	n/a
23	chr20:25130549-25130599	T-47D	breast:	n/a
24	chr20:25130549-25130599	HCF	heart:	n/a
25	chr20:25130549-25130599	HRE	kidney:	n/a
26	chr20:25130549-25130599	HL-60	blood:	n/a
27	chr20:25130549-25130599	HepG2	liver:	n/a
28	chr20:25130549-25130599	Caco-2	colon:	n/a
29	chr20:25130549-25130599	MCF-7	breast:	n/a
30	chr20:25130549-25130599	HNPCEpiC	eye:	n/a
31	chr20:25130549-25130599	NT2-D1	testis:	n/a
32	chr20:25130549-25130599	K562	blood:	n/a
33	chr20:25130549-25130599	SK-N-SH	brain:	n/a
34	chr20:25130549-25130599	ECC-1	luminal epithelium:	n/a
35	chr20:25130549-25130599	PrEC	prostate:	n/a
36	chr20:25130549-25130599	SK-N-SH_RA	brain:	n/a
37	chr20:25130549-25130599	NH-A	brain:	n/a
38	chr20:25130549-25130599	AoSMC	blood vessel:	n/a
39	chr20:25130549-25130599	AG04449	skin:	fetal
40	chr20:25130549-25130599	HMEC	breast:	n/a
41	chr20:25130549-25130599	PFSK-1	brain:	n/a
42	chr20:25130549-25130599	HIPEpiC	eye:	n/a
43	chr20:25130549-25130599	AG10803	skin:	n/a
44	chr20:25130549-25130599	HEK293	kidney:	embryo
45	chr20:25130549-25130599	SK-N-MC	brain:	n/a
46	chr20:25130549-25130599	RPTEC	kidney:	n/a
47	chr20:25130549-25130599	HRCEpiC	kidney:	n/a
48	chr20:25130549-25130599	Hela-S3	cervix:	n/a
49	chr20:25130549-25130599	SAEC	small airway:	n/a
50	chr20:25130549-25130599	AG09309	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25125843..25128254-chr20:25129443..25131955,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230725	TF binding region
ENSG00000230725	CpG island
ENSG00000230725	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs55879612	1.00[AMR][1000 genomes]
rs56063344	1.00[AMR][1000 genomes]
rs56343188	1.00[AMR][1000 genomes]
rs57359365	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57509861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58134777	1.00[AMR][1000 genomes]
rs6037066	1.00[AMR][1000 genomes]
rs6050450	1.00[AMR][1000 genomes]
rs6050467	1.00[AMR][1000 genomes]
rs6050480	1.00[AMR][1000 genomes]
rs61245897	1.00[AMR][1000 genomes]
rs73904004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904015	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904016	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904018	1.00[AMR][1000 genomes]
rs73904030	1.00[AMR][1000 genomes]
rs73904034	1.00[AMR][1000 genomes]
rs73904035	1.00[AMR][1000 genomes]
rs73904040	1.00[AMR][1000 genomes]
rs73906090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73907308	1.00[AMR][1000 genomes]
rs73907312	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25128600-25131600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:25128800-25131400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25128800-25131800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr20:25129400-25131400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
5	chr20:25129400-25131600	Enhancers	Fetal Brain Male	brain
6	chr20:25129600-25130600	Enhancers	Brain Cingulate Gyrus	brain
7	chr20:25129600-25131000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr20:25129600-25131200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:25129600-25131200	Enhancers	HSMMtube	muscle
10	chr20:25129800-25130600	Weak transcription	Brain Anterior Caudate	brain
11	chr20:25129800-25131000	Weak transcription	Ovary	ovary
12	chr20:25130000-25131000	Enhancers	Fetal Brain Female	brain
13	chr20:25130400-25130600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr20:25130400-25131000	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr20:25130400-25131400	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr20:25130400-25131600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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