Variant report

Variant	rs9462541
Chromosome Location	chr6:39386332-39386333
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	chr6:39380640..39382722-chr6:39382902..39386768,3	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1328386	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1410484	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1571362	0.93[EUR][1000 genomes]
rs1887711	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2395726	0.90[EUR][1000 genomes]
rs3734621	1.00[GIH][hapmap]
rs4714252	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6900461	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs913473	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs9369115	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9471075	1.00[GIH][hapmap]

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

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