Variant report

Variant	rs6049394
Chromosome Location	chr20:24081540-24081541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24080843..24083360-chr20:24088770..24090295,2	MCF-7	breast:
2	chr20:23870451..23870966-chr20:24081176..24081813,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1006194	0.84[EUR][1000 genomes]
rs2005624	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2013710	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2208012	0.94[EUR][1000 genomes]
rs6036640	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036644	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036645	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036650	0.97[EUR][1000 genomes]
rs6036653	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6036654	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6036664	0.94[EUR][1000 genomes]
rs6049389	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6049390	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6049392	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6049403	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049416	0.95[EUR][1000 genomes]
rs6049417	0.93[EUR][1000 genomes]
rs6049419	0.93[EUR][1000 genomes]
rs6114487	0.80[EUR][1000 genomes]
rs6114488	0.80[EUR][1000 genomes]
rs721314	0.93[EUR][1000 genomes]
rs761864	0.82[EUR][1000 genomes]
rs761865	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858140	0.91[EUR][1000 genomes]
rs858141	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs858144	0.97[EUR][1000 genomes]
rs858145	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs910775	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs974784	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs974785	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24076200-24082800	Weak transcription	HMEC	breast
2	chr20:24077800-24082800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr20:24079200-24081800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:24079200-24085200	Enhancers	NHEK	skin
5	chr20:24079400-24084400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:24079800-24082800	Weak transcription	A549	lung
7	chr20:24080000-24081600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:24080000-24083200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr20:24080200-24082600	Weak transcription	HUVEC	blood vessel
10	chr20:24080200-24083200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:24080400-24083000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr20:24081000-24081600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr20:24081000-24081600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr20:24081000-24081600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr20:24081000-24083800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr20:24081200-24081600	Enhancers	Pancreas	Pancrea
17	chr20:24081200-24081600	Enhancers	Dnd41	blood
18	chr20:24081200-24081800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:24081200-24084400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:24081400-24082800	Weak transcription	Osteobl	bone
21	chr20:24081400-24083000	Weak transcription	NH-A	brain
22	chr20:24081400-24083200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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