Variant report

Variant	rs2143857
Chromosome Location	chr20:11214401-11214402
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:11213940..11214546-chr4:16552592..16553227,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1473700	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1473701	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1473702	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1473703	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015108	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076643	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076644	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2076645	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2076646	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076647	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2143859	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2179827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207098	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207099	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2207100	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2223858	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2327366	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2327368	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2876220	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2876221	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35609472	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4384859	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4435520	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4449208	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4632419	0.88[ASN][1000 genomes]
rs4643605	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4813966	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813967	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813968	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4813969	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4813970	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4813971	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4813972	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033062	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033063	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033066	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033067	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6033068	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033069	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033070	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033071	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033072	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040435	0.85[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs6040436	0.86[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs6040442	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6040446	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040447	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040450	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040451	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040452	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040456	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6040458	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040459	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040460	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040461	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040463	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040464	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040465	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040466	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040469	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040470	0.87[ASN][1000 genomes]
rs6040471	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040472	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040473	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040474	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040475	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040477	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040479	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040480	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040481	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040482	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040486	0.88[EUR][1000 genomes]
rs6040487	0.85[EUR][1000 genomes]
rs6078105	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6078109	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6104726	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6108870	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6108871	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6108872	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6108876	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6108882	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs714690	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs714691	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs714692	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs761471	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761472	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926725	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs983251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs983252	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs983342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11207600-11216400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr20:11209400-11214600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:11209600-11214600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr20:11210800-11214800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr20:11210800-11215400	Weak transcription	Fetal Stomach	stomach
6	chr20:11211000-11214600	Weak transcription	Stomach Mucosa	stomach
7	chr20:11211000-11214800	Weak transcription	HSMM	muscle
8	chr20:11211000-11215200	Weak transcription	Fetal Kidney	kidney
9	chr20:11211000-11215400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr20:11211000-11215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr20:11211000-11215800	Weak transcription	Right Atrium	heart
12	chr20:11211000-11218600	Weak transcription	HSMMtube	muscle
13	chr20:11211200-11214600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:11211200-11214800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:11211200-11214800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr20:11211200-11214800	Weak transcription	NH-A	brain
17	chr20:11211200-11215200	Weak transcription	Osteobl	bone
18	chr20:11211200-11215400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr20:11211400-11216000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:11211800-11214600	Weak transcription	HUVEC	blood vessel
21	chr20:11211800-11214800	Weak transcription	HMEC	breast
22	chr20:11211800-11215600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr20:11211800-11215600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:11211800-11215800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr20:11212000-11215200	Weak transcription	NHEK	skin
26	chr20:11212200-11214600	Weak transcription	Fetal Lung	lung
27	chr20:11213000-11215000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr20:11213200-11214600	Weak transcription	GM12878-XiMat	blood
29	chr20:11213200-11216600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr20:11213400-11215800	Weak transcription	Fetal Muscle Leg	muscle
31	chr20:11213600-11214600	Weak transcription	Brain Anterior Caudate	brain
32	chr20:11213600-11214800	Weak transcription	Brain Angular Gyrus	brain
33	chr20:11213600-11216000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr20:11213800-11215800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:11214000-11215400	Enhancers	Brain Hippocampus Middle	brain
36	chr20:11214200-11215600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr20:11214400-11216800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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