Variant report

Variant	rs58272875
Chromosome Location	chr6:25012894-25012895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25011557..25013932-chr6:25024037..25026592,2	MCF-7	breast:
2	chr6:25008899..25010659-chr6:25012678..25014567,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000220517	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11964330	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12110508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12111569	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56772860	0.82[EUR][1000 genomes]
rs58446150	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58858607	0.82[EUR][1000 genomes]
rs59935869	0.82[EUR][1000 genomes]
rs60753079	0.82[EUR][1000 genomes]
rs73384104	0.82[EUR][1000 genomes]
rs73384131	0.82[EUR][1000 genomes]
rs73384137	0.82[EUR][1000 genomes]
rs73384148	0.82[EUR][1000 genomes]
rs73384155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384165	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73384168	1.00[EUR][1000 genomes]
rs73384170	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24997800-25016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25007000-25014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:25007400-25013200	Weak transcription	Fetal Lung	lung
4	chr6:25007400-25014800	Weak transcription	Fetal Brain Male	brain
5	chr6:25007400-25017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:25007600-25015000	Weak transcription	HSMMtube	muscle
7	chr6:25008000-25014600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:25008000-25014800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:25008000-25014800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:25008000-25015400	Weak transcription	Right Atrium	heart
11	chr6:25008000-25016600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr6:25008200-25013600	Weak transcription	GM12878-XiMat	blood
13	chr6:25008200-25015400	Weak transcription	Gastric	stomach
14	chr6:25009400-25015400	Weak transcription	Esophagus	oesophagus
15	chr6:25010000-25013400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:25010000-25016000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:25010000-25017400	Enhancers	Hela-S3	cervix
18	chr6:25010000-25018000	Enhancers	HMEC	breast
19	chr6:25010200-25013600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr6:25010200-25013800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:25010400-25014800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:25010400-25015200	Enhancers	NHDF-Ad	bronchial
23	chr6:25010400-25015800	Enhancers	NHLF	lung
24	chr6:25010400-25017200	Enhancers	Osteobl	bone
25	chr6:25010600-25013600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:25010600-25013600	Enhancers	NH-A	brain
27	chr6:25010600-25013800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:25010600-25014200	Weak transcription	Primary B cells from cord blood	blood
29	chr6:25010600-25015400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:25010600-25015400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:25010600-25015400	Weak transcription	Lung	lung
32	chr6:25010600-25015400	Weak transcription	Pancreas	Pancrea
33	chr6:25010800-25013400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:25010800-25013800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:25010800-25013800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:25010800-25013800	Enhancers	NHEK	skin
37	chr6:25011000-25013200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:25011000-25016800	Enhancers	HSMM	muscle
39	chr6:25011200-25013000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:25011200-25014600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:25011200-25015000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr6:25011200-25015000	Weak transcription	Fetal Thymus	thymus
43	chr6:25011200-25023400	Weak transcription	Thymus	Thymus
44	chr6:25011200-25035600	Weak transcription	Spleen	Spleen
45	chr6:25011600-25013000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:25011800-25014600	Weak transcription	Primary T cells from cord blood	blood
47	chr6:25011800-25015200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr6:25012000-25013000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:25012200-25018400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:25012400-25013400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links