Variant report

Variant	rs58478419
Chromosome Location	chr3:24492822-24492823
allele	A/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	chr3:24492099..24494371-chr3:24534161..24536408,2	MCF-7	breast:
2	chr3:24403805..24406463-chr3:24492311..24494276,2	MCF-7	breast:
3	chr3:24492821..24493789-chr3:24535289..24536029,2	MCF-7	breast:
4	chr3:24492726..24494917-chr3:24535454..24538001,3	MCF-7	breast:
5	chr3:24490789..24493603-chr3:24538186..24540704,2	K562	blood:
6	chr3:24490199..24493862-chr3:24535942..24541957,6	K562	blood:
7	chr3:24491764..24494170-chr3:24500245..24501846,2	K562	blood:
8	chr3:24492504..24495428-chr3:24499515..24502431,3	MCF-7	breast:
9	chr3:24492507..24495338-chr3:24496765..24498558,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000224822	Chromatin interaction
ENSG00000272554	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11711197	0.91[EUR][1000 genomes]
rs17014703	0.96[EUR][1000 genomes]
rs17014715	0.96[EUR][1000 genomes]
rs17014722	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59785554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792047	1.00[EUR][1000 genomes];1.00[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	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:33 , 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	chr3:24490200-24494000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:24490400-24493000	Enhancers	Hela-S3	cervix
10	chr3:24491000-24493000	Weak transcription	Left Ventricle	heart
11	chr3:24491000-24493000	Weak transcription	Pancreas	Pancrea
12	chr3:24491000-24493400	Weak transcription	Psoas Muscle	Psoas
13	chr3:24491000-24495200	Weak transcription	Right Ventricle	heart
14	chr3:24491000-24499400	Weak transcription	Aorta	Aorta
15	chr3:24491200-24493600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:24491200-24502200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:24491400-24496600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:24491600-24493400	Active TSS	HepG2	liver
19	chr3:24491800-24493600	Enhancers	Small Intestine	intestine
20	chr3:24492200-24493000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:24492200-24493000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:24492400-24493000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr3:24492400-24493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:24492400-24493400	Active TSS	Liver	Liver
25	chr3:24492400-24495800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:24492400-24498600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:24492400-24502200	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:24492600-24493000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:24492600-24493000	Weak transcription	Fetal Lung	lung
30	chr3:24492800-24493600	Enhancers	Adipose Nuclei	Adipose
31	chr3:24492800-24493800	Enhancers	A549	lung
32	chr3:24492800-24494000	Enhancers	Stomach Mucosa	stomach
33	chr3:24492800-24494200	Enhancers	Gastric	stomach

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