Variant report

Variant	rs6458115
Chromosome Location	chr6:39396537-39396538
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39383095..39385437-chr6:39394619..39397067,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10807207	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs10947809	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[ASN][1000 genomes]
rs10947810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs10947811	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs1106961	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs12527811	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[ASN][1000 genomes]
rs1328383	0.95[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1328388	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1328389	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1328390	0.96[ASN][1000 genomes]
rs1887713	0.95[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1999045	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs4142117	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4142118	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs4392720	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs4714250	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4714251	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs6458114	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6900629	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs6908396	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs72850620	0.83[ASN][1000 genomes]
rs7759557	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs9367004	0.89[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs9367005	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs9367006	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[ASN][1000 genomes]
rs9369114	0.95[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9380860	0.84[ASN][1000 genomes]
rs9394591	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9462543	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs9471089	0.83[ASN][1000 genomes]
rs9471090	0.95[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9471092	0.95[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs9471097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9471098	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv533806	chr6:39270073-39397337	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39385200-39398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:39389000-39398000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:39389400-39398200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:39390400-39399000	Weak transcription	Stomach Mucosa	stomach
5	chr6:39390600-39398800	Weak transcription	Lung	lung
6	chr6:39391000-39396600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:39392200-39397800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:39392600-39396600	Weak transcription	Spleen	Spleen
9	chr6:39392600-39397200	Enhancers	HMEC	breast
10	chr6:39393200-39397000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:39393200-39397000	Enhancers	NHEK	skin
12	chr6:39394200-39397000	Weak transcription	Fetal Lung	lung
13	chr6:39394200-39398400	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:39394200-39398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:39394200-39398800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:39394200-39399000	Weak transcription	Osteobl	bone
17	chr6:39394400-39396600	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:39394400-39397800	Weak transcription	Fetal Stomach	stomach
19	chr6:39394400-39398200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:39394400-39398400	Weak transcription	Brain Angular Gyrus	brain
21	chr6:39394400-39398600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:39394400-39398800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:39394400-39398800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:39394400-39399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:39394400-39399000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:39394400-39399000	Weak transcription	NH-A	brain
27	chr6:39394600-39398400	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:39394800-39398400	Weak transcription	Brain Anterior Caudate	brain
29	chr6:39394800-39398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:39395000-39397800	Weak transcription	NHDF-Ad	bronchial
31	chr6:39395000-39398200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:39395000-39398200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:39395200-39396600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:39395200-39397800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:39395200-39398600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:39395400-39396600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:39395400-39400000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:39395600-39396600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:39395600-39397000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:39395800-39397000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:39396000-39397000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr6:39396200-39397200	Enhancers	Brain Substantia Nigra	brain
43	chr6:39396200-39397800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:39396400-39396600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr6:39396400-39397400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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