Variant report

Variant	rs62255440
Chromosome Location	chr3:24480556-24480557
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24479242..24483220-chr3:24534441..24537229,5	MCF-7	breast:
2	chr3:24471972..24474391-chr3:24477875..24481695,3	K562	blood:
3	chr3:24473151..24475358-chr3:24479706..24482212,2	MCF-7	breast:
4	chr3:24476152..24478152-chr3:24480249..24482235,2	K562	blood:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000229756	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11707001	0.98[EUR][1000 genomes]
rs3456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4563353	0.82[EUR][1000 genomes]
rs62228823	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62228824	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62228825	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62228826	0.88[EUR][1000 genomes]
rs62228827	0.88[EUR][1000 genomes]
rs62228828	0.83[EUR][1000 genomes]
rs62255438	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62255439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62255441	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62255442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62255443	0.85[EUR][1000 genomes]
rs73034405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73034471	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73034493	1.00[AMR][1000 genomes];0.98[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	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24458800-24490200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:24474800-24483600	Enhancers	Fetal Intestine Large	intestine
3	chr3:24477000-24493000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:24477200-24490400	Weak transcription	Aorta	Aorta
5	chr3:24477200-24493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:24477400-24481800	Weak transcription	Right Atrium	heart
7	chr3:24477400-24482400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:24477800-24480800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:24478200-24482400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:24478200-24491400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:24478400-24490000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:24478400-24493400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:24479000-24482400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:24479400-24481400	Weak transcription	Liver	Liver
15	chr3:24479600-24480800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:24480000-24480800	Enhancers	Pancreas	Pancrea
17	chr3:24480000-24481000	Genic enhancers	Fetal Intestine Small	intestine
18	chr3:24480200-24480800	Enhancers	Left Ventricle	heart
19	chr3:24480200-24480800	Enhancers	Right Ventricle	heart
20	chr3:24480400-24480600	Enhancers	Esophagus	oesophagus
21	chr3:24480400-24480800	Enhancers	K562	blood
22	chr3:24480400-24482200	Weak transcription	HepG2	liver
23	chr3:24480400-24482400	Weak transcription	Psoas Muscle	Psoas

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