Variant report

Variant	rs10947809
Chromosome Location	chr6:39385182-39385183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39380640..39382722-chr6:39382902..39386768,3	MCF-7	breast:
2	chr6:39383095..39385437-chr6:39394619..39397067,2	MCF-7	breast:
3	chr6:39380506..39382532-chr6:39384473..39386042,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10807207	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10947810	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10947811	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1106961	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs12527811	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1328383	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[ASN][1000 genomes]
rs1328388	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs1328389	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs1328390	0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1887713	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs1999045	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4142117	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4142118	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4392720	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs4714250	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs4714251	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs6458114	0.81[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6458115	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[ASN][1000 genomes]
rs6900629	0.94[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6908396	1.00[CHB][hapmap]
rs72850620	0.92[ASN][1000 genomes]
rs7759557	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9367004	0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs9367005	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs9367006	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9369114	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[ASN][1000 genomes]
rs9380860	0.93[ASN][1000 genomes]
rs9394591	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[LWK][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs9462543	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9471089	0.92[ASN][1000 genomes]
rs9471090	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs9471092	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs9471097	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs9471098	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.93[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10947809	BRPF3	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39380000-39387600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:39381400-39390000	Weak transcription	Aorta	Aorta
3	chr6:39382400-39385400	Weak transcription	Fetal Brain Male	brain
4	chr6:39383200-39385200	Enhancers	Fetal Brain Female	brain
5	chr6:39383200-39385400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:39383200-39385600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:39383200-39386000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:39383400-39385800	Enhancers	HMEC	breast
9	chr6:39383400-39386000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:39383600-39385400	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr6:39383600-39385800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:39383800-39385200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:39383800-39385400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:39383800-39385400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:39383800-39385400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:39383800-39385400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:39383800-39385400	Enhancers	Brain Cingulate Gyrus	brain
18	chr6:39383800-39385400	Enhancers	Brain Substantia Nigra	brain
19	chr6:39383800-39385400	Enhancers	NHEK	skin
20	chr6:39383800-39385400	Enhancers	Osteobl	bone
21	chr6:39383800-39385600	Enhancers	NHDF-Ad	bronchial
22	chr6:39383800-39385800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:39383800-39385800	Enhancers	Stomach Smooth Muscle	stomach
24	chr6:39383800-39386000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:39383800-39386000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:39384000-39385200	Enhancers	NH-A	brain
27	chr6:39384000-39385400	Enhancers	HSMMtube	muscle
28	chr6:39384000-39385800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:39384200-39385200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr6:39384200-39385400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr6:39384200-39385400	Enhancers	Adipose Nuclei	Adipose
32	chr6:39384200-39387200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:39384200-39393200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:39384600-39385200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:39384600-39385400	Enhancers	Psoas Muscle	Psoas
36	chr6:39384600-39386000	Enhancers	Fetal Thymus	thymus
37	chr6:39384800-39385400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr6:39384800-39386000	Enhancers	Thymus	Thymus
39	chr6:39384800-39387200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:39384800-39389200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:39385000-39385200	Enhancers	Placenta	Placenta
42	chr6:39385000-39385200	Enhancers	Fetal Stomach	stomach
43	chr6:39385000-39385200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:39385000-39387200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:39385000-39387200	Weak transcription	Colon Smooth Muscle	Colon
46	chr6:39385000-39388400	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:39385000-39390200	Weak transcription	Brain Anterior Caudate	brain
48	chr6:39385000-39396400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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