Variant report

Variant	rs6023109
Chromosome Location	chr20:52930063-52930064
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52836744..52838613-chr20:52929896..52931739,2	MCF-7	breast:
2	chr20:52925826..52928871-chr20:52929162..52931995,4	MCF-7	breast:
3	chr20:52922402..52924055-chr20:52929439..52931142,2	MCF-7	breast:
4	chr20:52823879..52827026-chr20:52929276..52932008,3	MCF-7	breast:
5	chr20:52928133..52930874-chr20:52932134..52934559,2	K562	blood:
6	chr20:52927379..52930182-chr20:53082106..53084205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1382013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1477733	0.84[EUR][1000 genomes]
rs16999379	0.84[EUR][1000 genomes]
rs16999452	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16999466	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16999487	0.91[EUR][1000 genomes]
rs16999504	0.91[EUR][1000 genomes]
rs16999513	0.82[EUR][1000 genomes]
rs2219733	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28516647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2870321	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41428148	0.84[EUR][1000 genomes]
rs4289245	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4493332	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4541294	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4599177	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4619676	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56149353	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56268746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58025571	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58475917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58894404	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59811202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6013930	1.00[CEU][hapmap]
rs6013973	0.92[EUR][1000 genomes]
rs6013974	0.92[EUR][1000 genomes]
rs6013977	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6013980	0.91[EUR][1000 genomes]
rs6013981	0.91[EUR][1000 genomes]
rs6023065	0.92[EUR][1000 genomes]
rs6023077	0.84[EUR][1000 genomes]
rs6023111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023114	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023118	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023119	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023120	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023124	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023126	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023128	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6023139	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023144	0.91[EUR][1000 genomes]
rs6097927	0.82[EUR][1000 genomes]
rs61006519	0.84[EUR][1000 genomes]
rs723128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7265137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7265354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7272945	0.84[EUR][1000 genomes]
rs73137415	0.92[EUR][1000 genomes]
rs73137426	0.84[EUR][1000 genomes]
rs73137431	0.84[EUR][1000 genomes]
rs73137432	0.84[EUR][1000 genomes]
rs73137433	0.84[EUR][1000 genomes]
rs73137434	0.84[EUR][1000 genomes]
rs73137435	0.84[EUR][1000 genomes]
rs73137442	0.92[EUR][1000 genomes]
rs73137444	0.92[EUR][1000 genomes]
rs73137446	0.92[EUR][1000 genomes]
rs73137451	0.92[EUR][1000 genomes]
rs73137474	0.84[EUR][1000 genomes]
rs73137475	0.84[EUR][1000 genomes]
rs73137483	0.84[EUR][1000 genomes]
rs73139406	0.92[EUR][1000 genomes]
rs73139426	0.92[EUR][1000 genomes]
rs73139427	1.00[EUR][1000 genomes]
rs73139465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139467	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7347628	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8119798	1.00[AMR][1000 genomes];1.00[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	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	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
4	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:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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