Variant report

Variant	rs10273502
Chromosome Location	chr7:5230230-5230231
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	MXI1	chr7:5229583-5230487	GM12878	blood:	n/a	n/a
2	HA-E2F1	chr7:5229588-5230425	Hela-S3	cervix:	n/a	chr7:5229844-5229853 chr7:5229856-5229865
3	UBTF	chr7:5229863-5230542	K562	blood:	n/a	n/a
4	MAX	chr7:5230181-5230411	K562	blood:	n/a	n/a
5	NRF1	chr7:5229013-5230600	SK-N-SH	brain:	n/a	chr7:5229855-5229866 chr7:5229852-5229866 chr7:5229844-5229853 chr7:5229855-5229869 chr7:5229855-5229864 chr7:5229810-5229824
6	POLR2A	chr7:5229377-5230383	Hela-S3	cervix:	n/a	n/a
7	MAZ	chr7:5229570-5230500	K562	blood:	n/a	chr7:5229794-5229804
8	CTCF	chr7:5230220-5230370	HVMF	connective:	n/a	n/a
9	TAF1	chr7:5229551-5230356	HepG2	liver:	n/a	n/a
10	CTCF	chr7:5230200-5230350	GM12865	blood:	n/a	n/a
11	CTCF	chr7:5230200-5230350	GM12871	blood:	n/a	n/a
12	ZBTB7A	chr7:5230149-5230385	HepG2	liver:	n/a	n/a
13	CTCF	chr7:5230220-5230370	GM12865	blood:	n/a	n/a
14	ELF1	chr7:5230138-5230559	GM12878	blood:	n/a	n/a
15	CTCF	chr7:5230160-5230310	GM12869	blood:	n/a	n/a
16	POLR2A	chr7:5229474-5230590	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr7:5229020-5230440	HepG2	liver:	n/a	n/a
18	SIN3A	chr7:5229627-5230560	H1-hESC	embryonic stem cell:	n/a	chr7:5230261-5230274
19	MAX	chr7:5229555-5230460	Hela-S3	cervix:	n/a	chr7:5229794-5229804
20	MTA3	chr7:5230103-5230661	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:5229437-5230499	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr7:5229453-5230546	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr7:5229354-5230417	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr7:5230180-5230330	BJ	skin:	n/a	n/a
25	YY1	chr7:5229592-5230268	K562	blood:	n/a	chr7:5229844-5229853 chr7:5229850-5229861
26	CTCF	chr7:5230125-5230519	K562	blood:	n/a	n/a
27	CTCF	chr7:5230222-5230366	GM12891	blood:	n/a	n/a
28	POLR2A	chr7:5229451-5230235	H1-hESC	embryonic stem cell:	n/a	n/a
29	PAX5	chr7:5229596-5230333	GM12892	blood:	n/a	n/a
30	CTCF	chr7:5230220-5230370	GM12878	blood:	n/a	n/a
31	ZBTB7A	chr7:5229521-5230537	K562	blood:	n/a	chr7:5230136-5230147
32	CTCF	chr7:5230220-5230370	GM12870	blood:	n/a	n/a
33	POLR2A	chr7:5229363-5230337	MCF-7	breast:	n/a	n/a
34	CTCF	chr7:5230132-5230400	K562	blood:	n/a	n/a
35	SIN3AK20	chr7:5230151-5230350	HepG2	liver:	n/a	n/a
36	MAX	chr7:5229563-5230445	GM12878	blood:	n/a	chr7:5229794-5229804
37	SIN3A	chr7:5229701-5230446	GM12878	blood:	n/a	chr7:5230261-5230274
38	MAX	chr7:5229528-5230463	ECC-1	luminal epithelium:	n/a	chr7:5229794-5229804
39	RCOR1	chr7:5229488-5230482	K562	blood:	n/a	n/a
40	CTCF	chr7:5230200-5230350	HRPEpiC	eye:	n/a	n/a
41	POLR2A	chr7:5229116-5230663	K562	blood:	n/a	n/a
42	CTCF	chr7:5230180-5230330	GM12874	blood:	n/a	n/a
43	YY1	chr7:5230101-5230324	GM12878	blood:	n/a	chr7:5230279-5230293
44	CTCF	chr7:5230220-5230370	HUVEC	blood vessel:	n/a	n/a
45	CTCF	chr7:5230180-5230330	WERI-Rb-1	eye:	n/a	n/a
46	POLR2A	chr7:5229547-5230371	HUVEC	blood vessel:	n/a	n/a
47	YY1	chr7:5229522-5230520	K562	blood:	n/a	chr7:5229844-5229853 chr7:5229850-5229861 chr7:5230279-5230293
48	ELF1	chr7:5230123-5230360	K562	blood:	n/a	n/a
49	CTCF	chr7:5230140-5230290	HEK293	kidney:	n/a	n/a
50	ZBTB7A	chr7:5229946-5230630	K562	blood:	n/a	chr7:5230136-5230147

No.	Distal block	Cell Line	Cell type
1	chr7:5218548..5222992-chr7:5228147..5230588,3	MCF-7	breast:
2	chr16:3071236..3074140-chr7:5230121..5232796,2	MCF-7	breast:
3	chr1:11968100..11968787-chr7:5229394..5230254,2	Hela-S3	cervix:

Variant related genes	Relation type
WIPI2	TF binding region
ENSG00000131652	Chromatin interaction
ENSG00000103145	Chromatin interaction
ENSG00000202039	Chromatin interaction
ENSG00000199347	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10246437	0.84[EUR][1000 genomes]
rs10261990	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10269193	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11760558	0.83[AMR][1000 genomes]
rs11763996	0.83[AMR][1000 genomes]
rs28393199	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28514595	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28619195	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28649271	0.83[AMR][1000 genomes]
rs28757707	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59601349	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73048032	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73048054	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
5	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv1031007	chr7:5101766-5262695	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
9	nsv1015639	chr7:5209510-5255399	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv887390	chr7:5224407-5411296	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5228800-5231000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:5229200-5230400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:5229200-5230400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr7:5229200-5230400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr7:5229200-5230400	Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr7:5229200-5230400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:5229200-5230400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:5229200-5230400	Active TSS	Brain Cingulate Gyrus	brain
9	chr7:5229200-5230400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:5229200-5230400	Active TSS	Fetal Brain Female	brain
11	chr7:5229200-5230400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr7:5229200-5230600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:5229200-5230600	Active TSS	Brain Hippocampus Middle	brain
14	chr7:5229200-5230800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:5229200-5230800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:5229200-5230800	Active TSS	Brain Anterior Caudate	brain
17	chr7:5229200-5230800	Active TSS	Fetal Intestine Large	intestine
18	chr7:5229200-5231000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr7:5229200-5231000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr7:5229200-5231000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr7:5229200-5231000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:5229200-5231000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr7:5229200-5231000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:5229200-5231000	Active TSS	Stomach Mucosa	stomach
25	chr7:5229200-5231000	Active TSS	A549	lung
26	chr7:5229200-5231000	Active TSS	Hela-S3	cervix
27	chr7:5229200-5231400	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr7:5229200-5231400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:5229200-5231600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr7:5229400-5230400	Active TSS	Primary B cells from cord blood	blood
31	chr7:5229400-5230400	Active TSS	Primary T cells from cord blood	blood
32	chr7:5229400-5230400	Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr7:5229400-5230400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:5229400-5230400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:5229400-5230400	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr7:5229400-5230400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr7:5229400-5230400	Active TSS	Brain Germinal Matrix	brain
38	chr7:5229400-5230600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr7:5229400-5230600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:5229400-5230600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:5229400-5230600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:5229400-5230600	Active TSS	Aorta	Aorta
43	chr7:5229400-5230600	Active TSS	Brain Angular Gyrus	brain
44	chr7:5229400-5230600	Active TSS	Fetal Lung	lung
45	chr7:5229400-5230600	Active TSS	NH-A	brain
46	chr7:5229400-5230600	Active TSS	Osteobl	bone
47	chr7:5229400-5230800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr7:5229400-5230800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:5229400-5230800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:5229400-5230800	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links