Variant report

Variant	rs6023386
Chromosome Location	chr20:53206034-53206035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53000318..53001983-chr20:53203861..53206076,2	MCF-7	breast:
2	chr20:53201780..53208417-chr20:53214130..53221252,9	MCF-7	breast:
3	chr20:53185049..53189714-chr20:53202808..53207275,5	MCF-7	breast:
4	chr20:53200153..53202638-chr20:53204182..53206369,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10485784	0.82[EUR][1000 genomes]
rs17327539	0.82[EUR][1000 genomes]
rs2169707	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28663252	0.86[EUR][1000 genomes]
rs55960128	0.82[EUR][1000 genomes]
rs56371656	0.84[EUR][1000 genomes]
rs58298733	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60030360	0.81[AMR][1000 genomes]
rs6014066	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6014067	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6014073	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6014074	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6014075	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6014076	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6014077	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6014078	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6014080	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023382	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6023383	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6023384	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023385	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023387	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023388	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023394	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023397	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023398	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023401	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6023403	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6091925	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098093	0.80[EUR][1000 genomes]
rs6098099	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6098103	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6098104	1.00[CEU][hapmap]
rs6098105	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6098111	0.87[CEU][hapmap]
rs6098118	0.85[CEU][hapmap]
rs67907005	0.82[EUR][1000 genomes]
rs7269966	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73140147	0.82[EUR][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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53201800-53208000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr20:53202000-53211800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr20:53202200-53230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:53202800-53208200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr20:53203800-53210200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
7	chr20:53206000-53206600	ZNF genes & repeats	Aorta	Aorta

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