Variant report

Variant	rs9462543
Chromosome Location	chr6:39387344-39387345
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	chr6:39387298..39389611-chr6:39391657..39393931,2	MCF-7	breast:

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];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10947809	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]
rs10947810	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10947811	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1106961	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12527811	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[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];0.82[ASN][1000 genomes]
rs1328389	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs1328390	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1887713	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs1999045	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4142117	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[ASN][1000 genomes]
rs4142118	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4392720	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs4714250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4714251	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6458114	0.81[CHB][hapmap];0.91[ASN][1000 genomes]
rs6458115	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs6900629	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs6908396	1.00[CHB][hapmap]
rs72850620	0.92[ASN][1000 genomes]
rs7759557	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9367004	0.89[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9367005	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9367006	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[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];1.00[CHD][hapmap];0.93[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];0.90[CHD][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
rs9462543	BRPF3	cis	cerebellum	SCAN

Chromatin state (count:40 , 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	chr6:39384200-39393200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:39384800-39389200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:39385000-39388400	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:39385000-39390200	Weak transcription	Brain Anterior Caudate	brain
7	chr6:39385000-39396400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:39385200-39387400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:39385200-39387600	Weak transcription	Fetal Stomach	stomach
10	chr6:39385200-39390000	Weak transcription	Placenta	Placenta
11	chr6:39385200-39390000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:39385200-39398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:39385400-39388200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:39385400-39388400	Weak transcription	Brain Substantia Nigra	brain
15	chr6:39385400-39388600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:39385400-39388600	Weak transcription	Psoas Muscle	Psoas
17	chr6:39385400-39389400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:39385400-39389800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:39385400-39389800	Weak transcription	Adipose Nuclei	Adipose
20	chr6:39385400-39390200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:39385400-39390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:39385400-39390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:39385400-39393200	Weak transcription	NHEK	skin
24	chr6:39385600-39389200	Weak transcription	NHDF-Ad	bronchial
25	chr6:39385600-39389800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:39385800-39389200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:39385800-39389400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:39385800-39389400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:39385800-39389600	Weak transcription	HMEC	breast
30	chr6:39386000-39389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:39386000-39389200	Weak transcription	Fetal Thymus	thymus
32	chr6:39386000-39389400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:39387200-39387600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:39387200-39387600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:39387200-39387600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:39387200-39387800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:39387200-39388000	Enhancers	Colon Smooth Muscle	Colon
38	chr6:39387200-39389400	Enhancers	Rectal Smooth Muscle	rectum
39	chr6:39387200-39389800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr6:39387200-39391000	Enhancers	Stomach Smooth Muscle	stomach

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