Variant report

Variant	rs6824446
Chromosome Location	chr4:125859264-125859265
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	chr4:125857080..125860001-chr4:125867292..125869846,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10022194	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10031287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1021628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722357	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729566	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11732928	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11945096	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1384817	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1483592	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1483599	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1483601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1553094	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1553095	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564721	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17184111	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17788496	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28477204	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28607791	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72920861	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695258	1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9997123	1.00[CHB][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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125844800-125860600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:125856200-125860600	Enhancers	Fetal Muscle Leg	muscle
3	chr4:125856200-125866800	Enhancers	Hela-S3	cervix
4	chr4:125856400-125860400	Weak transcription	NHEK	skin
5	chr4:125856600-125859800	Enhancers	Fetal Heart	heart
6	chr4:125856600-125860600	Weak transcription	Right Ventricle	heart
7	chr4:125857600-125859600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr4:125857600-125862600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:125857800-125859600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr4:125857800-125861400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:125858000-125859400	Weak transcription	Osteobl	bone
12	chr4:125858000-125860000	Weak transcription	HUVEC	blood vessel
13	chr4:125858000-125860200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:125858000-125860200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:125858000-125860400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:125858000-125860400	Weak transcription	Lung	lung
17	chr4:125858000-125860400	Weak transcription	Right Atrium	heart
18	chr4:125858000-125860800	Weak transcription	NH-A	brain
19	chr4:125858000-125861200	Weak transcription	Adipose Nuclei	Adipose
20	chr4:125858000-125861400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:125858000-125865000	Weak transcription	Ovary	ovary
22	chr4:125858000-125868000	Weak transcription	Pancreas	Pancrea
23	chr4:125858200-125859400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:125858200-125859400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:125858200-125859400	Weak transcription	HSMM	muscle
26	chr4:125858200-125860200	Weak transcription	NHLF	lung
27	chr4:125858200-125861400	Weak transcription	Stomach Mucosa	stomach
28	chr4:125858200-125867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:125858400-125859400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:125858600-125859400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:125858600-125859600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:125858600-125859600	Enhancers	Left Ventricle	heart
33	chr4:125858600-125859800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr4:125858600-125861000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:125858800-125859400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr4:125858800-125859600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr4:125858800-125859600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr4:125859000-125859400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:125859000-125859400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:125859000-125859400	Enhancers	Psoas Muscle	Psoas
41	chr4:125859000-125859600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:125859000-125861200	Weak transcription	Fetal Stomach	stomach
43	chr4:125859000-125861600	Weak transcription	Fetal Kidney	kidney
44	chr4:125859200-125859400	Enhancers	Esophagus	oesophagus
45	chr4:125859200-125859400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr4:125859200-125859600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:125859200-125859600	Enhancers	HSMMtube	muscle
48	chr4:125859200-125859800	Enhancers	Gastric	stomach
49	chr4:125859200-125861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:125859200-125862800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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