Variant report

Variant	rs6040469
Chromosome Location	chr20:11228296-11228297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1473700	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473702	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473703	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015108	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2076643	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076644	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076645	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076646	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2076647	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2143857	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2143859	0.88[ASN][1000 genomes]
rs2179827	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2207098	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2207099	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207100	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2223858	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327366	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327368	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2876220	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2876221	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4384859	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4435520	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4449208	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4632419	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4643605	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813966	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4813967	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4813968	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813969	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813970	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813972	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813974	0.81[CHB][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs4813975	0.83[AMR][1000 genomes]
rs6033062	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033063	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033066	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033067	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033068	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033069	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033070	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033071	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033072	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040435	0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs6040436	0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs6040442	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6040446	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040447	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040450	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040451	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040452	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040456	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6040458	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040459	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040460	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040461	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040463	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040464	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040465	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040466	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040470	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040471	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040472	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040473	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040474	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040475	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040477	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040479	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6040480	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6040481	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6040482	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6040486	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040487	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040489	0.87[AMR][1000 genomes]
rs6040490	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6078105	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6078109	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6104726	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6108870	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6108871	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6108872	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6108876	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6108882	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs714690	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs714691	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs714692	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761471	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs761472	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs926725	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs983251	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs983252	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs983342	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs983343	0.84[EUR][1000 genomes];0.88[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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11216200-11228400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr20:11216200-11238800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:11225400-11231000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:11226000-11228600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr20:11226600-11229400	Enhancers	Brain Germinal Matrix	brain
6	chr20:11227000-11228800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:11227000-11229400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:11227000-11230800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:11227400-11235000	Weak transcription	Fetal Kidney	kidney
10	chr20:11227600-11229400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:11227600-11229600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr20:11227800-11228400	Enhancers	Fetal Brain Male	brain
13	chr20:11227800-11228800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr20:11227800-11229600	Enhancers	Fetal Brain Female	brain
15	chr20:11228000-11230000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr20:11228200-11228400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr20:11228200-11229400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr20:11228200-11229800	Enhancers	Fetal Lung	lung
19	chr20:11228200-11230600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr20:11228200-11230800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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