Variant report

Variant	rs6040667
Chromosome Location	chr20:11409150-11409151
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:11408827..11411317-chr20:11413467..11415014,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1009747	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1009748	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11697311	0.92[EUR][1000 genomes]
rs11697340	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11698313	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11699470	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11699490	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13038146	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17189710	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17261909	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2143871	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207116	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2207117	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2327412	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2876227	0.82[ASN][1000 genomes]
rs4315598	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4444612	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4813995	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6033135	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6033137	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6033138	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040619	0.98[EUR][1000 genomes]
rs6040625	0.97[EUR][1000 genomes]
rs6040630	0.98[EUR][1000 genomes]
rs6040633	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040634	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6040636	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040637	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040638	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040644	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040646	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040647	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040648	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040649	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6040654	0.93[EUR][1000 genomes]
rs6040655	0.89[EUR][1000 genomes]
rs6040657	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6040658	0.92[EUR][1000 genomes]
rs6040660	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6040661	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6040663	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6040665	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6040666	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6040668	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6131203	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6131206	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6131208	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134243	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134246	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62191867	0.97[EUR][1000 genomes]
rs62191868	0.98[EUR][1000 genomes]
rs742827	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv432099	chr20:11371093-11476900	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1058734	chr20:11389232-11479953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11394600-11409800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:11408000-11409800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr20:11408000-11410000	Weak transcription	HSMMtube	muscle
4	chr20:11408000-11410600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:11408000-11410800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:11408000-11415000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:11408200-11410000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr20:11408200-11410800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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