Variant report

Variant	rs62228823
Chromosome Location	chr3:24492354-24492355
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24492099..24494371-chr3:24534161..24536408,2	MCF-7	breast:
2	chr3:24403805..24406463-chr3:24492311..24494276,2	MCF-7	breast:
3	chr3:24481444..24484786-chr3:24488715..24492560,4	K562	blood:
4	chr3:24490789..24493603-chr3:24538186..24540704,2	K562	blood:
5	chr3:24490199..24493862-chr3:24535942..24541957,6	K562	blood:
6	chr3:24491764..24494170-chr3:24500245..24501846,2	K562	blood:

Variant related genes	Relation type
ENSG00000224822	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000272554	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	0.96[EUR][1000 genomes]
rs3456	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4563353	0.80[EUR][1000 genomes]
rs62228824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62228825	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62228826	0.90[EUR][1000 genomes]
rs62228827	0.90[EUR][1000 genomes]
rs62228828	0.85[EUR][1000 genomes]
rs62255438	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62255439	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62255440	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62255441	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62255442	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62255443	0.83[EUR][1000 genomes]
rs73034405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73034471	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73034493	1.00[AMR][1000 genomes];1.00[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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24477000-24493000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:24477200-24493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:24478400-24493400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:24482600-24493000	Weak transcription	Right Atrium	heart
5	chr3:24488600-24493000	Weak transcription	K562	blood
6	chr3:24488800-24497800	Enhancers	Fetal Intestine Small	intestine
7	chr3:24489200-24497400	Enhancers	Fetal Intestine Large	intestine
8	chr3:24490200-24492400	Enhancers	Colon Smooth Muscle	Colon
9	chr3:24490200-24492400	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr3:24490200-24494000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:24490400-24492600	Enhancers	Fetal Lung	lung
12	chr3:24490400-24493000	Enhancers	Hela-S3	cervix
13	chr3:24491000-24493000	Weak transcription	Left Ventricle	heart
14	chr3:24491000-24493000	Weak transcription	Pancreas	Pancrea
15	chr3:24491000-24493400	Weak transcription	Psoas Muscle	Psoas
16	chr3:24491000-24495200	Weak transcription	Right Ventricle	heart
17	chr3:24491000-24499400	Weak transcription	Aorta	Aorta
18	chr3:24491200-24492400	Enhancers	Adipose Nuclei	Adipose
19	chr3:24491200-24493600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:24491200-24502200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:24491400-24496600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr3:24491600-24493400	Active TSS	HepG2	liver
23	chr3:24491800-24492400	Flanking Active TSS	Liver	Liver
24	chr3:24491800-24492400	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr3:24491800-24493600	Enhancers	Small Intestine	intestine
26	chr3:24492000-24492400	Enhancers	A549	lung
27	chr3:24492000-24492600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:24492200-24492400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:24492200-24492400	Enhancers	Gastric	stomach
30	chr3:24492200-24492400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr3:24492200-24492400	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr3:24492200-24492800	Weak transcription	Stomach Mucosa	stomach
33	chr3:24492200-24493000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:24492200-24493000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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