Variant report

Variant	rs4712879
Chromosome Location	chr6:25017704-25017705
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	chr6:24718678..24720864-chr6:25017128..25019517,2	K562	blood:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

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

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

rs_ID	r²[population]
rs10806997	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10946741	0.82[EUR][1000 genomes]
rs10946742	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10946743	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2394360	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4712880	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6918101	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][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	chr6:25010000-25018000	Enhancers	HMEC	breast
2	chr6:25011200-25023400	Weak transcription	Thymus	Thymus
3	chr6:25011200-25035600	Weak transcription	Spleen	Spleen
4	chr6:25012200-25018400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:25012600-25018400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr6:25012600-25018600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:25012800-25018600	Enhancers	Primary B cells from peripheral blood	blood
8	chr6:25013000-25018200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:25013600-25017800	Weak transcription	NH-A	brain
10	chr6:25013800-25018400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:25014200-25018800	Enhancers	Primary B cells from cord blood	blood
12	chr6:25014400-25018200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:25014600-25018400	Enhancers	Primary T cells from cord blood	blood
14	chr6:25014800-25018000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:25014800-25018400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:25015000-25018400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr6:25015200-25018200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr6:25015200-25018400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:25015400-25018200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:25015600-25017800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:25015600-25018200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:25015600-25018600	Enhancers	NHEK	skin
23	chr6:25015600-25023600	Weak transcription	Fetal Thymus	thymus
24	chr6:25015800-25017800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:25015800-25017800	Weak transcription	GM12878-XiMat	blood
26	chr6:25015800-25018400	Enhancers	Primary hematopoietic stem cells	blood
27	chr6:25015800-25018600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:25015800-25023800	Weak transcription	Dnd41	blood
29	chr6:25015800-25027000	Weak transcription	Esophagus	oesophagus
30	chr6:25016000-25017800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr6:25016000-25017800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr6:25016000-25018400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:25016400-25018200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:25016400-25018400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr6:25016400-25018600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:25016600-25017800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:25016600-25017800	Weak transcription	Lung	lung
38	chr6:25016600-25018000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:25016600-25018000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:25016600-25018200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr6:25016600-25018200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr6:25016600-25018200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:25016600-25018600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:25016800-25017800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:25016800-25017800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:25016800-25017800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:25016800-25018000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr6:25016800-25018200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:25016800-25022400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:25017000-25018200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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