Variant report

Variant	rs6023119
Chromosome Location	chr20:52937053-52937054
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52823148..52825997-chr20:52936130..52937975,3	MCF-7	breast:
2	chr20:52838097..52840122-chr20:52937035..52938814,2	MCF-7	breast:
3	chr20:52823575..52826757-chr20:52934438..52938480,4	MCF-7	breast:
4	chr16:84732268..84735213-chr20:52936747..52939132,2	MCF-7	breast:
5	chr20:52889394..52890221-chr20:52936512..52937186,2	MCF-7	breast:
6	chr20:52935516..52937390-chr20:53262812..53265904,3	MCF-7	breast:
7	chr20:52835803..52837047-chr20:52936331..52937389,14	MCF-7	breast:
8	chr20:52933134..52935057-chr20:52935363..52937322,2	MCF-7	breast:
9	chr20:52835882..52837224-chr20:52936327..52937749,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000103194	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1382013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1477733	0.84[EUR][1000 genomes]
rs16999379	0.84[EUR][1000 genomes]
rs16999452	0.96[AFR][1000 genomes];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	0.96[AFR][1000 genomes];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	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4541294	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4599177	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4619676	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56149353	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56268746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58025571	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58475917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58894404	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59811202	0.98[AFR][1000 genomes];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]
rs6023109	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023113	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023114	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023118	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023120	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023124	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023126	0.96[AFR][1000 genomes];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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7265137	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7265354	0.98[AFR][1000 genomes];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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139467	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73139477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7347628	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8119798	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52936400-52937400	Enhancers	Osteobl	bone
2	chr20:52936600-52937200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr20:52936600-52937600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:52936800-52937200	Enhancers	Hela-S3	cervix
5	chr20:52937000-52938200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr20:52937000-52940400	Weak transcription	Ovary	ovary

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