Variant report

Variant	rs309873
Chromosome Location	chr4:48336820-48336821
allele	C/G
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:
2	chr4:48330630..48332591-chr4:48335471..48337148,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11723080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs309868	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309875	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309887	0.87[AMR][1000 genomes]
rs418214	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695369	0.83[ASN][1000 genomes]
rs55784928	0.81[ASN][1000 genomes]
rs55860639	0.83[ASN][1000 genomes]
rs62309393	0.84[ASN][1000 genomes]
rs62309398	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62309399	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62309400	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309401	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309402	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6833004	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv275483	chr4:48336371-48338344	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 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	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
2	chr4:48331000-48337400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:48331600-48339400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:48331600-48339600	Weak transcription	Stomach Mucosa	stomach
5	chr4:48331600-48340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:48332600-48339200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:48333000-48341800	Weak transcription	A549	lung
8	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
9	chr4:48333800-48338400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:48334000-48341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:48334200-48337200	Weak transcription	NHLF	lung
12	chr4:48334200-48339600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:48334200-48340200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:48334200-48342000	Weak transcription	Fetal Heart	heart
15	chr4:48334200-48342000	Weak transcription	HSMM	muscle
16	chr4:48334200-48342200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:48334400-48337000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:48334400-48342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:48334800-48337000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:48334800-48341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:48335600-48338400	Enhancers	Hela-S3	cervix
23	chr4:48335600-48339600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:48335800-48342000	Weak transcription	Fetal Kidney	kidney
25	chr4:48336000-48337600	Enhancers	Placenta	Placenta
26	chr4:48336000-48338000	Weak transcription	NHDF-Ad	bronchial
27	chr4:48336200-48338200	Enhancers	Psoas Muscle	Psoas
28	chr4:48336400-48338400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:48336400-48338800	Weak transcription	NHEK	skin
30	chr4:48336400-48339000	Weak transcription	HMEC	breast
31	chr4:48336400-48339400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:48336400-48342000	Weak transcription	Osteobl	bone
33	chr4:48336600-48337000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr4:48336600-48338400	Enhancers	Fetal Muscle Leg	muscle
35	chr4:48336800-48337400	Enhancers	HSMMtube	muscle
36	chr4:48336800-48337600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:48336800-48337600	Flanking Active TSS	K562	blood
38	chr4:48336800-48337800	Enhancers	Fetal Thymus	thymus
39	chr4:48336800-48339200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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