Variant report

Variant	rs4712878
Chromosome Location	chr6:25009321-25009322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24979064..24981330-chr6:25006890..25009589,2	K562	blood:
2	chr6:25008899..25010659-chr6:25012678..25014567,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10806997	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10946741	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10946742	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10946743	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs11758900	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12194111	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1410689	0.83[EUR][1000 genomes]
rs1536768	0.82[EUR][1000 genomes]
rs2183067	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712880	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs6918101	0.89[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs6922006	0.88[EUR][1000 genomes]
rs7748247	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs983223	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[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:69 , 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	chr6:25004200-25011200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:25004400-25011800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:25006200-25011200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr6:25006400-25010800	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:25006400-25011200	Enhancers	Thymus	Thymus
7	chr6:25006600-25010800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:25006600-25011200	Enhancers	Fetal Thymus	thymus
9	chr6:25006800-25010600	Enhancers	Lung	lung
10	chr6:25007000-25009400	Enhancers	Esophagus	oesophagus
11	chr6:25007000-25014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:25007200-25010400	Weak transcription	NHLF	lung
13	chr6:25007200-25010600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:25007200-25010800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr6:25007200-25010800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:25007200-25011200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:25007200-25011600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:25007400-25010000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:25007400-25010600	Weak transcription	NH-A	brain
20	chr6:25007400-25010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:25007400-25010800	Enhancers	Primary T cells fromperipheralblood	blood
22	chr6:25007400-25011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:25007400-25012800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:25007400-25013200	Weak transcription	Fetal Lung	lung
25	chr6:25007400-25014800	Weak transcription	Fetal Brain Male	brain
26	chr6:25007400-25017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:25007600-25010400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:25007600-25011000	Weak transcription	HSMM	muscle
29	chr6:25007600-25015000	Weak transcription	HSMMtube	muscle
30	chr6:25007800-25010400	Weak transcription	NHDF-Ad	bronchial
31	chr6:25007800-25010400	Weak transcription	Osteobl	bone
32	chr6:25007800-25010600	Enhancers	Primary B cells from cord blood	blood
33	chr6:25007800-25010800	Weak transcription	NHEK	skin
34	chr6:25007800-25011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:25007800-25011000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:25007800-25011200	Enhancers	Spleen	Spleen
37	chr6:25008000-25009600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:25008000-25010000	Weak transcription	Hela-S3	cervix
39	chr6:25008000-25010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:25008000-25010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:25008000-25010600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:25008000-25010600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:25008000-25010600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:25008000-25010600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:25008000-25011000	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:25008000-25014600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:25008000-25014800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:25008000-25014800	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:25008000-25015400	Weak transcription	Right Atrium	heart
50	chr6:25008000-25016600	Enhancers	Monocytes-CD14+_RO01746	blood

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