Variant report

Variant	rs17059297
Chromosome Location	chr4:174257455-174257456
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:174253089-174257840	PBDE	blood:	n/a	n/a
2	POLR2A	chr4:174253253-174257499	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:174088355..174091772-chr4:174254077..174258410,8	K562	blood:
2	chr4:174252933..174259053-chr4:174284716..174299463,25	MCF-7	breast:
3	chr4:174088713..174091772-chr4:174254390..174258410,4	K562	blood:
4	chr4:174256552..174259513-chr4:174261559..174263260,2	MCF-7	breast:
5	chr4:174254894..174256484-chr4:174257318..174259644,2	MCF-7	breast:
6	chr4:174250771..174257645-chr4:174286907..174294441,15	MCF-7	breast:
7	chr4:174245727..174260507-chr4:174283013..174295498,65	K562	blood:
8	chr4:174248778..174262653-chr4:174278408..174298501,82	K562	blood:

No data

Variant related genes	Relation type
HMGB2	TF binding region
ENSG00000164104	Chromatin interaction
ENSG00000245213	Chromatin interaction
ENSG00000272870	Chromatin interaction
ENSG00000164105	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17059270	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17059275	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28387978	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28581661	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28605939	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59610063	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60501935	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6553690	1.00[EUR][1000 genomes]
rs6553691	1.00[EUR][1000 genomes]
rs6810397	0.91[EUR][1000 genomes]
rs6810604	1.00[EUR][1000 genomes]
rs6814914	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816923	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6824485	1.00[EUR][1000 genomes]
rs6854376	0.86[ASN][1000 genomes]
rs6856630	1.00[EUR][1000 genomes]
rs72999548	1.00[EUR][1000 genomes]
rs73001541	0.86[ASN][1000 genomes]
rs73001544	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73001549	1.00[EUR][1000 genomes]
rs73001568	1.00[EUR][1000 genomes]
rs73003329	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73003331	0.86[ASN][1000 genomes]
rs73872518	0.91[EUR][1000 genomes]
rs7691279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv966552	chr4:174248506-174259305	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174254400-174257800	Active TSS	Thymus	Thymus
2	chr4:174254600-174257800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:174254800-174257600	Active TSS	Fetal Thymus	thymus
4	chr4:174254800-174257600	Active TSS	K562	blood
5	chr4:174256600-174257600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:174256600-174258000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:174256600-174258000	Flanking Active TSS	Dnd41	blood
8	chr4:174256800-174280400	Weak transcription	Aorta	Aorta
9	chr4:174257000-174257800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:174257000-174258000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:174257000-174258000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:174257000-174258000	Enhancers	Osteobl	bone
13	chr4:174257000-174258200	Enhancers	Hela-S3	cervix
14	chr4:174257000-174258400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:174257000-174258800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:174257000-174259000	Enhancers	NHDF-Ad	bronchial
17	chr4:174257000-174259200	Enhancers	Fetal Heart	heart
18	chr4:174257000-174261800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:174257000-174264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:174257000-174264400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:174257200-174257600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr4:174257200-174257600	Flanking Active TSS	A549	lung
23	chr4:174257200-174257800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:174257200-174257800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:174257200-174257800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:174257200-174257800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:174257200-174257800	Enhancers	Fetal Lung	lung
28	chr4:174257200-174257800	Enhancers	HMEC	breast
29	chr4:174257200-174257800	Enhancers	NHEK	skin
30	chr4:174257200-174258000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:174257200-174258000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:174257200-174258000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:174257200-174258000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:174257200-174258000	Flanking Active TSS	GM12878-XiMat	blood
35	chr4:174257200-174258000	Enhancers	HepG2	liver
36	chr4:174257200-174258600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:174257200-174258800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:174257200-174264400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:174257400-174257600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:174257400-174257600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:174257400-174257600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr4:174257400-174257800	Active TSS	Brain Germinal Matrix	brain
43	chr4:174257400-174257800	Flanking Active TSS	NHLF	lung
44	chr4:174257400-174258000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr4:174257400-174258000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
46	chr4:174257400-174258600	Weak transcription	HSMM	muscle

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