Variant report

Variant	rs3920009
Chromosome Location	chr10:25337420-25337421
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	chr10:25304583..25307026-chr10:25335686..25338076,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185875	Chromatin interaction
ENSG00000151023	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11014310	1.00[AMR][1000 genomes]
rs1158057	1.00[AMR][1000 genomes]
rs12098488	1.00[AMR][1000 genomes]
rs1352983	0.82[YRI][hapmap]
rs16925204	1.00[AMR][1000 genomes]
rs16925206	1.00[AMR][1000 genomes]
rs16925213	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16925221	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16925231	0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34736361	1.00[AMR][1000 genomes]
rs7091416	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7901799	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550224	chr10:25335854-25385858	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25335600-25338000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr10:25336000-25337800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:25336000-25337800	Enhancers	HMEC	breast
4	chr10:25336000-25338000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:25336000-25338000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:25336200-25337600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:25336200-25337600	Enhancers	Osteobl	bone
8	chr10:25336200-25337800	Enhancers	NHEK	skin
9	chr10:25336200-25338200	Enhancers	Fetal Intestine Small	intestine
10	chr10:25336400-25337600	Enhancers	HSMM	muscle
11	chr10:25336400-25338200	Enhancers	Brain Anterior Caudate	brain
12	chr10:25336600-25338000	Enhancers	HSMMtube	muscle
13	chr10:25337000-25338000	Enhancers	Brain Substantia Nigra	brain
14	chr10:25337000-25338200	Enhancers	Fetal Intestine Large	intestine
15	chr10:25337200-25337600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:25337200-25337600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
17	chr10:25337200-25337800	Enhancers	Ovary	ovary
18	chr10:25337200-25338200	Enhancers	Duodenum Mucosa	Duodenum
19	chr10:25337400-25337600	Enhancers	Fetal Brain Female	brain
20	chr10:25337400-25337600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr10:25337400-25338200	Enhancers	K562	blood
22	chr10:25337400-25348200	Weak transcription	Placenta Amnion	Placenta Amnion

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