Variant report

Variant	rs6458989
Chromosome Location	chr6:54108748-54108749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53850708..53851695-chr6:54108679..54109745,3	MCF-7	breast:
2	chr17:56708364..56710438-chr6:54107125..54109891,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10080252	0.88[ASN][1000 genomes]
rs10155669	0.80[ASN][1000 genomes]
rs10456172	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10484647	0.83[ASN][1000 genomes]
rs1074639	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948803	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150874	0.85[ASN][1000 genomes]
rs11757700	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661972	0.88[ASN][1000 genomes]
rs1340664	0.82[ASN][1000 genomes]
rs1340665	0.80[ASN][1000 genomes]
rs1342831	0.88[ASN][1000 genomes]
rs1417389	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1575220	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16869492	0.88[ASN][1000 genomes]
rs16885091	0.88[ASN][1000 genomes]
rs17755375	0.82[ASN][1000 genomes]
rs17828437	0.83[ASN][1000 genomes]
rs1856829	0.88[ASN][1000 genomes]
rs2145758	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2180931	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275769	0.88[ASN][1000 genomes]
rs2275770	0.88[ASN][1000 genomes]
rs2792646	0.82[ASN][1000 genomes]
rs34961553	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41530746	0.80[ASN][1000 genomes]
rs4329099	0.88[ASN][1000 genomes]
rs4712059	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55689719	0.88[ASN][1000 genomes]
rs59132111	0.88[ASN][1000 genomes]
rs62397397	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6458988	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924913	0.88[ASN][1000 genomes]
rs6932559	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6934602	0.88[ASN][1000 genomes]
rs6937413	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73741487	0.88[ASN][1000 genomes]
rs7740331	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816382	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816383	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816384	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816385	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9283919	0.88[ASN][1000 genomes]
rs9296740	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9296741	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296742	0.88[ASN][1000 genomes]
rs9296743	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395916	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395918	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9464034	0.82[ASN][1000 genomes]
rs9464042	0.88[ASN][1000 genomes]
rs9464043	0.88[ASN][1000 genomes]
rs9464045	0.88[ASN][1000 genomes]
rs9464046	0.88[ASN][1000 genomes]
rs9474762	0.88[ASN][1000 genomes]
rs9474765	0.88[ASN][1000 genomes]
rs9474766	0.88[ASN][1000 genomes]
rs9474768	0.88[ASN][1000 genomes]
rs9474771	0.88[ASN][1000 genomes]
rs9474772	0.88[ASN][1000 genomes]
rs9474773	0.88[ASN][1000 genomes]
rs9474774	0.88[ASN][1000 genomes]
rs9885975	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017633	chr6:53935336-54118476	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1020961	chr6:54101801-54133709	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1020329	chr6:54103966-54129147	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54101000-54119800	Weak transcription	Right Ventricle	heart
2	chr6:54101400-54120800	Weak transcription	Psoas Muscle	Psoas
3	chr6:54102200-54119800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:54104000-54108800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:54104000-54119800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:54104200-54110200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:54104200-54120800	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:54107600-54108800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:54108400-54108800	Enhancers	Left Ventricle	heart
10	chr6:54108600-54109000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:54108600-54109000	Enhancers	Fetal Heart	heart

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