Variant report

Variant	rs16999643
Chromosome Location	chr20:53066809-53066810
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:53052476..53054956-chr20:53065782..53068416,3	MCF-7	breast:
2	chr17:57914261..57916683-chr20:53066420..53069406,2	MCF-7	breast:
3	chr20:53057603..53060260-chr20:53065002..53067209,2	K562	blood:
4	chr20:53065913..53067901-chr20:53077459..53079852,2	MCF-7	breast:
5	chr20:53046706..53049615-chr20:53062995..53067004,4	MCF-7	breast:
6	chr20:53066739..53069116-chr20:53078549..53080137,4	MCF-7	breast:
7	chr20:53065974..53067555-chr20:53070867..53073344,2	MCF-7	breast:
8	chr20:53061996..53063880-chr20:53065895..53070016,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12329481	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs13042185	0.88[CEU][hapmap]
rs13042986	0.89[CEU][hapmap]
rs13044898	0.88[CEU][hapmap]
rs1330017	0.88[CEU][hapmap]
rs55665963	0.85[EUR][1000 genomes]
rs58143732	0.83[EUR][1000 genomes]
rs6014019	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014020	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6014027	0.89[CEU][hapmap]
rs6014032	0.88[CEU][hapmap]
rs6023244	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6023245	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs6023247	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6023248	0.80[EUR][1000 genomes]
rs6023251	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023253	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023254	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023258	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023262	0.85[AMR][1000 genomes]
rs6023263	0.85[AMR][1000 genomes]
rs6023272	0.89[CEU][hapmap]
rs6023273	0.89[CEU][hapmap]
rs6023274	0.89[CEU][hapmap]
rs6023275	0.89[CEU][hapmap]
rs6023276	0.89[CEU][hapmap]
rs6023291	0.88[CEU][hapmap]
rs6023307	0.89[CEU][hapmap]
rs6023309	0.89[CEU][hapmap]
rs60780716	0.83[EUR][1000 genomes]
rs6091886	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6091891	0.88[CEU][hapmap]
rs6097986	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6097987	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097988	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6097998	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6097999	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6098002	0.85[AMR][1000 genomes]
rs6098006	0.89[CEU][hapmap]
rs6098007	0.89[CEU][hapmap]
rs6098008	0.89[CEU][hapmap]
rs6098009	0.88[CEU][hapmap]
rs6098011	0.89[CEU][hapmap]
rs7264053	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7264143	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7271481	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7271579	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73141254	0.98[EUR][1000 genomes]
rs73141258	0.85[EUR][1000 genomes]
rs922398	0.88[CEU][hapmap]

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	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	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53066800-53067200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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