Variant report

Variant	rs59720516
Chromosome Location	chr4:48334229-48334230
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48329154..48338368-chr4:48340296..48348694,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11735909	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11932711	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1472970	0.80[ASN][1000 genomes]
rs2008107	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2353296	0.80[ASN][1000 genomes]
rs4340766	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57233179	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58275144	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58351439	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58620171	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59336353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61010385	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6447628	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6835303	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6835363	0.80[ASN][1000 genomes]
rs6835615	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6845740	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6857308	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7682629	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs925288	0.84[EUR][1000 genomes];0.84[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	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48330000-48336200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
3	chr4:48330200-48335200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:48330800-48336000	Enhancers	NHDF-Ad	bronchial
5	chr4:48331000-48336400	Enhancers	NHEK	skin
6	chr4:48331000-48337400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:48331200-48335000	Enhancers	HMEC	breast
8	chr4:48331200-48336400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:48331600-48335600	Weak transcription	K562	blood
10	chr4:48331600-48339400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:48331600-48339600	Weak transcription	Stomach Mucosa	stomach
12	chr4:48331600-48340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:48332000-48334600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:48332200-48334400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:48332200-48334400	Enhancers	HSMMtube	muscle
16	chr4:48332600-48334800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:48332600-48339200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:48332800-48334400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr4:48333000-48334400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:48333000-48341800	Weak transcription	A549	lung
21	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
22	chr4:48333400-48334800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:48333600-48334400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr4:48333600-48334400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr4:48333800-48334400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:48333800-48338400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:48334000-48341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:48334200-48334800	Enhancers	Psoas Muscle	Psoas
29	chr4:48334200-48335000	Enhancers	Placenta	Placenta
30	chr4:48334200-48335600	Weak transcription	Hela-S3	cervix
31	chr4:48334200-48335600	Weak transcription	Osteobl	bone
32	chr4:48334200-48336600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:48334200-48337200	Weak transcription	NHLF	lung
34	chr4:48334200-48339600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:48334200-48340200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:48334200-48342000	Weak transcription	Fetal Heart	heart
37	chr4:48334200-48342000	Weak transcription	HSMM	muscle
38	chr4:48334200-48342200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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