Variant report

Variant	rs28499181
Chromosome Location	chr3:54389434-54389435
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11713798	0.91[EUR][1000 genomes]
rs11715872	0.88[EUR][1000 genomes]
rs1375517	0.88[EUR][1000 genomes]
rs1868505	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56027715	0.88[EUR][1000 genomes]
rs59598269	0.86[EUR][1000 genomes]
rs6445649	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445650	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445652	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7427395	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7431093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835975	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[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	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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54380000-54391200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:54383400-54392600	Weak transcription	Right Ventricle	heart
3	chr3:54384000-54392400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:54387200-54392000	Enhancers	Fetal Lung	lung
5	chr3:54387200-54392600	Enhancers	Ovary	ovary
6	chr3:54387200-54394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:54387400-54390200	Enhancers	Left Ventricle	heart
8	chr3:54387400-54391800	Enhancers	Fetal Brain Male	brain
9	chr3:54387400-54392000	Enhancers	Adipose Nuclei	Adipose
10	chr3:54387600-54389600	Enhancers	Colon Smooth Muscle	Colon
11	chr3:54387600-54394800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:54387600-54394800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:54387600-54396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:54387800-54393800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:54388000-54390200	Weak transcription	Fetal Brain Female	brain
16	chr3:54388200-54391800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:54388600-54389600	Enhancers	Fetal Muscle Leg	muscle
18	chr3:54388600-54389800	Weak transcription	Brain Anterior Caudate	brain
19	chr3:54388800-54389600	Enhancers	Aorta	Aorta
20	chr3:54388800-54389800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:54388800-54389800	Weak transcription	Fetal Stomach	stomach
22	chr3:54388800-54391200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:54388800-54395400	Enhancers	Hela-S3	cervix
24	chr3:54389000-54391200	Enhancers	Psoas Muscle	Psoas
25	chr3:54389200-54389800	Enhancers	Brain Hippocampus Middle	brain
26	chr3:54389200-54390400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:54389200-54390800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:54389200-54392000	Enhancers	Right Atrium	heart
29	chr3:54389400-54390000	Enhancers	Esophagus	oesophagus
30	chr3:54389400-54390400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:54389400-54390400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:54389400-54393600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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