Variant report

Variant	rs1553093
Chromosome Location	chr4:125857023-125857024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:125825931..125828528-chr4:125854551..125857392,2	MCF-7	breast:
2	chr4:125632485..125635693-chr4:125853926..125858479,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151458	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10022194	0.84[GIH][hapmap]
rs10031287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722357	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732928	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945096	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384817	0.85[ASN][1000 genomes]
rs1483592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483599	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1553094	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553095	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17184111	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17788496	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477204	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28607791	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6824446	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72920861	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695258	1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307556	0.84[GIH][hapmap]

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	nsv1011752	chr4:125708756-125932456	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1001338	chr4:125708756-126103293	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv830050	chr4:125717858-125888563	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125844800-125860600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:125845600-125857600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:125852400-125857200	Weak transcription	HSMMtube	muscle
4	chr4:125852800-125857800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:125853000-125857400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:125853000-125857400	Weak transcription	Osteobl	bone
7	chr4:125853200-125859000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:125854200-125857600	Weak transcription	Pancreas	Pancrea
9	chr4:125855200-125858000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:125855600-125858000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:125855600-125858200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:125856200-125857600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:125856200-125858000	Enhancers	Brain Germinal Matrix	brain
14	chr4:125856200-125859000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr4:125856200-125859200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:125856200-125860600	Enhancers	Fetal Muscle Leg	muscle
17	chr4:125856200-125866800	Enhancers	Hela-S3	cervix
18	chr4:125856400-125860400	Weak transcription	NHEK	skin
19	chr4:125856600-125857400	Weak transcription	Ovary	ovary
20	chr4:125856600-125857800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:125856600-125857800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:125856600-125858200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:125856600-125858800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:125856600-125858800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:125856600-125859000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:125856600-125859800	Enhancers	Fetal Heart	heart
27	chr4:125856600-125860600	Weak transcription	Right Ventricle	heart
28	chr4:125856800-125858000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:125856800-125858400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:125856800-125858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr4:125856800-125858600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:125856800-125859000	Enhancers	Fetal Lung	lung
33	chr4:125857000-125858000	Enhancers	Adipose Nuclei	Adipose
34	chr4:125857000-125858200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:125857000-125858200	Enhancers	NHLF	lung

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