Variant report

Variant	rs6023139
Chromosome Location	chr20:52953876-52953877
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52932133..52934142-chr20:52951112..52954074,2	MCF-7	breast:
2	chr20:52937969..52941351-chr20:52951827..52954635,3	MCF-7	breast:
3	chr20:52824041..52826237-chr20:52953149..52955469,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1382013	0.82[EUR][1000 genomes]
rs16999452	0.82[EUR][1000 genomes]
rs16999466	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16999487	0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16999504	0.91[EUR][1000 genomes]
rs16999513	0.82[EUR][1000 genomes]
rs2219733	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs28373824	0.82[EUR][1000 genomes]
rs28516647	0.82[EUR][1000 genomes]
rs2870321	0.82[EUR][1000 genomes]
rs4289245	0.82[EUR][1000 genomes]
rs4493332	0.82[EUR][1000 genomes]
rs4541294	0.82[EUR][1000 genomes]
rs4599177	0.82[EUR][1000 genomes]
rs4619676	0.82[EUR][1000 genomes]
rs56149353	0.82[EUR][1000 genomes]
rs56268746	0.82[EUR][1000 genomes]
rs58025571	0.82[EUR][1000 genomes]
rs58475917	0.82[EUR][1000 genomes]
rs58894404	0.82[EUR][1000 genomes]
rs59811202	0.82[EUR][1000 genomes]
rs6013930	1.00[CEU][hapmap]
rs6013973	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6013974	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6013977	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6013980	0.91[EUR][1000 genomes]
rs6013981	0.91[EUR][1000 genomes]
rs6023077	0.84[EUR][1000 genomes]
rs6023109	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023111	0.82[EUR][1000 genomes]
rs6023113	0.82[EUR][1000 genomes]
rs6023114	0.82[EUR][1000 genomes]
rs6023116	0.82[EUR][1000 genomes]
rs6023118	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023119	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023120	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023124	0.82[EUR][1000 genomes]
rs6023126	0.82[EUR][1000 genomes]
rs6023128	1.00[CEU][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6023144	0.91[EUR][1000 genomes]
rs6097927	1.00[EUR][1000 genomes]
rs723128	0.82[EUR][1000 genomes]
rs7265137	0.82[EUR][1000 genomes]
rs7265354	0.82[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]
rs73139427	0.82[EUR][1000 genomes]
rs73139465	0.82[EUR][1000 genomes]
rs73139467	0.82[EUR][1000 genomes]
rs73139469	0.82[EUR][1000 genomes]
rs73139472	0.82[EUR][1000 genomes]
rs73139477	0.82[EUR][1000 genomes]
rs7347628	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8119798	0.82[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:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52951000-52957200	Weak transcription	Gastric	stomach
2	chr20:52952200-52955000	Weak transcription	HUVEC	blood vessel
3	chr20:52952400-52956600	Weak transcription	Osteobl	bone
4	chr20:52952400-52956800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:52952400-52956800	Weak transcription	Muscle Satellite Cultured Cells	--

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