Variant report

Variant	rs4953454
Chromosome Location	chr2:47290028-47290029
allele	C/T
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	CTCF	chr2:47289960-47290110	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr2:47289137-47290443	SK-N-SH_RA	brain:	n/a	chr2:47290098-47290110
3	POLR2A	chr2:47289616-47290106	H1-neurons	neurons:	n/a	n/a
4	MAX	chr2:47289330-47290187	SK-N-SH	brain:	n/a	chr2:47289917-47289926
5	YY1	chr2:47289404-47290617	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr2:47289462-47290160	H1-neurons	neurons:	n/a	n/a
7	CTCF	chr2:47289940-47290090	SK-N-SH_RA	brain:	n/a	n/a
8	GATA2	chr2:47289303-47290132	SH-SY5Y	brain:	n/a	chr2:47289456-47289467 chr2:47289579-47289586
9	YY1	chr2:47289386-47290136	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr2:47289380-47290297	SK-N-SH_RA	brain:	n/a	chr2:47289594-47289604
11	REST	chr2:47289428-47290165	SK-N-SH	brain:	n/a	n/a
12	RAD21	chr2:47289427-47290239	SK-N-SH_RA	brain:	n/a	chr2:47290098-47290110
13	MXI1	chr2:47287939-47291917	SK-N-SH	brain:	n/a	chr2:47289917-47289932 chr2:47289915-47289930
14	EP300	chr2:47289369-47290338	SK-N-SH_RA	brain:	n/a	chr2:47289594-47289604
15	EP300	chr2:47287499-47292041	SK-N-SH	brain:	n/a	chr2:47288383-47288392 chr2:47290945-47290958 chr2:47289594-47289604
16	POLR2A	chr2:47289299-47290284	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47271461..47273944-chr2:47289960..47292872,2	K562	blood:
2	chr2:47287750..47290295-chr2:47291902..47294626,3	K562	blood:
3	chr2:47288474..47290884-chr2:47401391..47403774,3	K562	blood:
4	chr2:47288795..47291567-chr2:47291902..47294947,3	K562	blood:
5	chr2:47270985..47273817-chr2:47288372..47290875,2	MCF-7	breast:
6	chr2:47283603..47286484-chr2:47288928..47291971,4	K562	blood:
7	chr2:47285787..47290884-chr2:47401621..47403774,5	K562	blood:

Variant related genes	Relation type
ENSG00000225187	TF binding region
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10460536	0.82[AMR][1000 genomes]
rs12465751	0.83[LWK][hapmap];0.81[YRI][hapmap]
rs13392391	1.00[ASN][1000 genomes]
rs17036168	0.88[GIH][hapmap]
rs17036208	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280648	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2436767	0.81[YRI][hapmap]
rs2436768	0.81[YRI][hapmap]
rs2692220	0.81[YRI][hapmap]
rs3739099	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4953455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59787338	0.82[AMR][1000 genomes]
rs60395026	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61377948	0.84[AMR][1000 genomes]
rs6734192	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6750227	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72875120	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 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	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:47270800-47296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:47272200-47292000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:47274800-47292800	Weak transcription	Hela-S3	cervix
6	chr2:47278600-47290800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:47282000-47293400	Enhancers	Brain Substantia Nigra	brain
8	chr2:47284400-47296400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:47284400-47296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:47284600-47290600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:47284600-47296000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:47284600-47298400	Strong transcription	Thymus	Thymus
13	chr2:47284800-47292600	Weak transcription	Small Intestine	intestine
14	chr2:47285000-47292800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:47285000-47295000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:47285000-47295200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:47285000-47295400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:47285200-47291000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr2:47285200-47295800	Strong transcription	Primary T cells from cord blood	blood
20	chr2:47285400-47292400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:47285400-47292600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:47285600-47291600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:47285600-47292400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:47285800-47291800	Weak transcription	Fetal Kidney	kidney
25	chr2:47285800-47292600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:47286000-47292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:47286000-47292800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:47286400-47290600	Strong transcription	A549	lung
29	chr2:47286400-47292000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:47286400-47295400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:47286600-47291000	Strong transcription	Pancreas	Pancrea
32	chr2:47286600-47292000	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr2:47286600-47295000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:47286800-47290200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:47286800-47292600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:47286800-47296000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:47286800-47296600	Strong transcription	Fetal Thymus	thymus
38	chr2:47287200-47291000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr2:47287400-47292000	Strong transcription	GM12878-XiMat	blood
40	chr2:47287400-47296200	Strong transcription	Primary B cells from cord blood	blood
41	chr2:47287600-47290200	Strong transcription	HepG2	liver
42	chr2:47287600-47291600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:47287600-47291800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:47287600-47291800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:47287600-47292200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:47287600-47292200	Genic enhancers	Adipose Nuclei	Adipose
47	chr2:47287600-47293400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:47287800-47290200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:47287800-47290600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:47287800-47292000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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