Variant report

Variant	rs6456643
Chromosome Location	chr6:24995003-24995004
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24994587..24995258-chr6:25017941..25018872,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1571425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2149453	1.00[AMR][1000 genomes]
rs4712874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6456642	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7744690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7758891	1.00[AMR][1000 genomes]
rs7771790	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24984200-24995200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24986000-24996600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:24986400-24995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:24986400-24995400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:24986600-24996600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:24987600-25000200	Weak transcription	Lung	lung
7	chr6:24992200-24995200	Weak transcription	Thymus	Thymus
8	chr6:24992200-24995600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:24992200-24996600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:24992200-24996600	Weak transcription	Fetal Thymus	thymus
11	chr6:24992200-24996600	Weak transcription	Stomach Mucosa	stomach
12	chr6:24992200-24998000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:24992200-25006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:24992400-24996600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:24992600-24995200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:24992600-24995600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:24992600-24995600	Weak transcription	Fetal Heart	heart
18	chr6:24992600-24995800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:24992600-24996400	Weak transcription	Hela-S3	cervix
20	chr6:24992600-24996600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:24992600-24996800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:24992600-25000000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:24992800-24995200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr6:24992800-24996400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:24992800-24996400	Weak transcription	Primary T cells from cord blood	blood
26	chr6:24992800-24996400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:24992800-24996600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:24992800-24996600	Weak transcription	Dnd41	blood
29	chr6:24992800-24996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:24992800-24997400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:24993000-24995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:24993000-24997000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:24993400-24995400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:24993800-24995200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:24993800-24995800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr6:24994000-24996600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:24994600-24995400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr6:24994600-24995600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr6:24994600-24996600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr6:24994600-24996800	Enhancers	Primary B cells from cord blood	blood
41	chr6:24994800-24996000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr6:24994800-24996400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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