Variant report

Variant	rs4563353
Chromosome Location	chr3:24490129-24490130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24481444..24484786-chr3:24488715..24492560,4	K562	blood:
2	chr3:24489242..24492071-chr3:24535616..24538264,2	MCF-7	breast:
3	chr3:24460201..24461830-chr3:24489473..24491006,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10510544	0.86[JPT][hapmap]
rs11707001	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11714673	0.86[JPT][hapmap]
rs2043581	0.86[JPT][hapmap]
rs3456	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs35317485	0.91[ASN][1000 genomes]
rs35947386	0.91[ASN][1000 genomes]
rs4241527	0.85[JPT][hapmap]
rs4350869	0.81[ASN][1000 genomes]
rs4566480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858616	0.91[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs4858617	0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs56101205	0.88[ASN][1000 genomes]
rs62228823	0.80[EUR][1000 genomes]
rs62228824	0.80[EUR][1000 genomes]
rs62255439	0.82[EUR][1000 genomes]
rs62255440	0.82[EUR][1000 genomes]
rs62255442	0.82[EUR][1000 genomes]
rs62255443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034405	0.82[EUR][1000 genomes]
rs73034493	0.80[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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24458800-24490200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:24477000-24493000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:24477200-24490400	Weak transcription	Aorta	Aorta
4	chr3:24477200-24493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:24478200-24491400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:24478400-24493400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:24482600-24493000	Weak transcription	Right Atrium	heart
8	chr3:24483000-24490400	Weak transcription	Left Ventricle	heart
9	chr3:24483000-24490400	Weak transcription	Pancreas	Pancrea
10	chr3:24483000-24490400	Weak transcription	Right Ventricle	heart
11	chr3:24486400-24490800	Weak transcription	Psoas Muscle	Psoas
12	chr3:24488000-24490200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:24488000-24491000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:24488200-24490200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:24488400-24490200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:24488600-24490400	Weak transcription	Gastric	stomach
17	chr3:24488600-24493000	Weak transcription	K562	blood
18	chr3:24488800-24492200	Enhancers	Stomach Mucosa	stomach
19	chr3:24488800-24497800	Enhancers	Fetal Intestine Small	intestine
20	chr3:24489200-24497400	Enhancers	Fetal Intestine Large	intestine
21	chr3:24489400-24490600	Enhancers	Small Intestine	intestine
22	chr3:24489400-24491200	Enhancers	HepG2	liver
23	chr3:24490000-24490400	Flanking Active TSS	Liver	Liver
24	chr3:24490000-24490800	Enhancers	Duodenum Mucosa	Duodenum

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