Variant report

Variant	rs6040552
Chromosome Location	chr20:11319524-11319525
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10048850	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16992379	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16992385	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092643	0.91[EUR][1000 genomes]
rs2207102	0.94[EUR][1000 genomes]
rs2207111	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813983	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56880002	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56916303	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343506	0.88[EUR][1000 genomes]
rs57494012	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57530621	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57628024	0.88[EUR][1000 genomes]
rs58745127	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60059631	0.94[EUR][1000 genomes]
rs6033098	0.94[EUR][1000 genomes]
rs6033105	0.89[EUR][1000 genomes]
rs6033115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60399139	0.89[EUR][1000 genomes]
rs6040519	0.94[EUR][1000 genomes]
rs6040525	0.94[EUR][1000 genomes]
rs6040535	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040544	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040549	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040560	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040561	0.91[AFR][1000 genomes]
rs60517966	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074282	0.82[AFR][1000 genomes]
rs61045178	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6108901	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6108902	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61252470	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73243915	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243929	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243934	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243975	0.94[EUR][1000 genomes]
rs73243981	0.94[EUR][1000 genomes]
rs73244000	0.94[EUR][1000 genomes]
rs73245616	0.91[EUR][1000 genomes]
rs73245627	0.91[EUR][1000 genomes]
rs73261557	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982209	1.00[EUR][1000 genomes];1.00[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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11312000-11323200	Weak transcription	Psoas Muscle	Psoas
2	chr20:11314000-11323000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:11317800-11319600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr20:11318400-11323400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr20:11318600-11323400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:11319200-11319600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr20:11319400-11319600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:11319400-11319600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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