Variant report

Variant	rs9864089
Chromosome Location	chr3:54388490-54388491
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:54375027..54375647-chr3:54388254..54389644,4	MCF-7	breast:
2	chr3:54375117..54375902-chr3:54387751..54388811,4	MCF-7	breast:
3	chr3:54375027..54375990-chr3:54387842..54389644,8	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12632182	1.00[YRI][hapmap]
rs13319005	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28560392	1.00[AMR][1000 genomes]
rs9809130	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9816445	1.00[YRI][hapmap]
rs9818719	1.00[YRI][hapmap]
rs9822780	1.00[YRI][hapmap]
rs9836702	1.00[AMR][1000 genomes]
rs9844238	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9853670	1.00[AMR][1000 genomes]
rs9858447	1.00[AMR][1000 genomes]
rs9859898	1.00[YRI][hapmap]
rs9861079	1.00[AMR][1000 genomes]
rs9863977	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9874563	1.00[YRI][hapmap]
rs9877208	1.00[YRI][hapmap];1.00[AMR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54378800-54389000	Weak transcription	Psoas Muscle	Psoas
2	chr3:54380000-54391200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:54383400-54392600	Weak transcription	Right Ventricle	heart
4	chr3:54384000-54392400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:54387200-54392000	Enhancers	Fetal Lung	lung
6	chr3:54387200-54392600	Enhancers	Ovary	ovary
7	chr3:54387200-54394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:54387400-54389400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:54387400-54390200	Enhancers	Left Ventricle	heart
10	chr3:54387400-54391800	Enhancers	Fetal Brain Male	brain
11	chr3:54387400-54392000	Enhancers	Adipose Nuclei	Adipose
12	chr3:54387600-54388800	Enhancers	Fetal Stomach	stomach
13	chr3:54387600-54388800	Flanking Active TSS	Hela-S3	cervix
14	chr3:54387600-54389200	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr3:54387600-54389600	Enhancers	Colon Smooth Muscle	Colon
16	chr3:54387600-54394800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:54387600-54394800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:54387600-54396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:54387800-54388600	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:54387800-54388800	Weak transcription	Aorta	Aorta
21	chr3:54387800-54389000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:54387800-54393800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:54388000-54389200	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:54388000-54389200	Weak transcription	Right Atrium	heart
25	chr3:54388000-54390200	Weak transcription	Fetal Brain Female	brain
26	chr3:54388200-54391800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:54388400-54388600	Enhancers	Brain Anterior Caudate	brain

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