Variant report

Variant	rs62228859
Chromosome Location	chr3:24517174-24517175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:24514725..24517450-chr3:24535783..24537402,2	MCF-7	breast:
2	chr3:24510569..24514476-chr3:24514887..24518486,4	K562	blood:
3	chr3:24516329..24518836-chr3:24531927..24534617,2	MCF-7	breast:
4	chr3:24503594..24506625-chr3:24513720..24517968,3	MCF-7	breast:
5	chr3:24516699..24519082-chr3:24520454..24523738,3	K562	blood:
6	chr3:24514431..24517573-chr3:24535246..24537303,3	K562	blood:
7	chr3:24510569..24514143-chr3:24516133..24518576,3	K562	blood:
8	chr3:24516134..24523238-chr3:24531050..24538059,11	MCF-7	breast:
9	chr3:24516844..24518628-chr3:24560760..24563117,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000265028	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs62228828	0.83[EUR][1000 genomes]
rs62228829	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62228850	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62228852	0.86[EUR][1000 genomes]
rs62228853	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62228855	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62228856	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62230460	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62230461	0.84[EUR][1000 genomes]
rs62230463	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62230464	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs721216	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73036459	1.00[AMR][1000 genomes]
rs73036460	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9845983	0.86[EUR][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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24499600-24526800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:24503200-24517200	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:24504600-24517400	Weak transcription	Right Ventricle	heart
4	chr3:24509600-24531000	Weak transcription	Fetal Lung	lung
5	chr3:24510000-24517400	Weak transcription	NHDF-Ad	bronchial
6	chr3:24511000-24517400	Weak transcription	Fetal Intestine Small	intestine
7	chr3:24513600-24517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:24513600-24517400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:24513600-24517400	Weak transcription	Adipose Nuclei	Adipose
10	chr3:24513800-24517400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:24514000-24517400	Weak transcription	Liver	Liver
12	chr3:24514000-24517400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:24514200-24517400	Weak transcription	Psoas Muscle	Psoas
14	chr3:24514600-24517400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:24514800-24517400	Weak transcription	Hela-S3	cervix
16	chr3:24515600-24517400	Weak transcription	Left Ventricle	heart
17	chr3:24515600-24533200	Weak transcription	Stomach Mucosa	stomach
18	chr3:24515800-24517400	Weak transcription	HepG2	liver
19	chr3:24515800-24517800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:24517000-24517800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:24517000-24518200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:24517000-24518400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:24517000-24518600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:24517000-24518600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:24517000-24519000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:24517000-24519600	Enhancers	Skeletal Muscle Male	skeletal muscle

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