Variant report

Variant	rs17004039
Chromosome Location	chr4:80572391-80572392
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	chr4:80562829..80565369-chr4:80570389..80573368,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11929731	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11931506	0.81[EUR][1000 genomes]
rs11935255	1.00[CEU][hapmap]
rs17003979	1.00[CEU][hapmap]
rs17004018	0.81[EUR][1000 genomes]
rs17004021	0.81[EUR][1000 genomes]
rs4348124	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4389606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56659743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58972167	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59575356	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	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1005152	chr4:80549659-80814456	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80568400-80572600	Weak transcription	Fetal Brain Male	brain
2	chr4:80568400-80572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:80571400-80573000	Enhancers	NHDF-Ad	bronchial
4	chr4:80571600-80572400	Enhancers	Colon Smooth Muscle	Colon
5	chr4:80571600-80574000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:80571600-80574800	Enhancers	NH-A	brain
7	chr4:80571800-80573200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:80571800-80573600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:80571800-80573600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:80571800-80575400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:80572000-80572400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:80572000-80572400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:80572000-80572400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:80572000-80572400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr4:80572000-80572400	Enhancers	HMEC	breast
16	chr4:80572000-80572400	Flanking Active TSS	Osteobl	bone
17	chr4:80572000-80572600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:80572000-80572800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:80572000-80572800	Enhancers	HSMMtube	muscle
20	chr4:80572000-80572800	Flanking Active TSS	NHEK	skin
21	chr4:80572000-80573000	Enhancers	H9 Cell Line	embryonic stem cell
22	chr4:80572000-80573200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:80572000-80573200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:80572000-80573600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:80572000-80573800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:80572000-80574200	Enhancers	Fetal Lung	lung
27	chr4:80572000-80574800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:80572000-80575400	Enhancers	Rectal Smooth Muscle	rectum
29	chr4:80572200-80572400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:80572200-80572400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr4:80572200-80572400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:80572200-80572600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr4:80572200-80572600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr4:80572200-80572600	Active TSS	Stomach Smooth Muscle	stomach
35	chr4:80572200-80572600	Flanking Active TSS	HUVEC	blood vessel
36	chr4:80572200-80572800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:80572200-80572800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr4:80572200-80573000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:80572200-80573000	Enhancers	Fetal Stomach	stomach
40	chr4:80572200-80573000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr4:80572200-80574000	Enhancers	Hela-S3	cervix

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