Variant report

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:53469992..53472672-chr20:53482676..53485188,2	MCF-7	breast:
2	chr20:53469608..53471175-chr20:53474621..53476655,2	MCF-7	breast:
3	chr20:53467255..53472616-chr20:53474478..53478474,4	MCF-7	breast:
4	chr20:53465234..53466924-chr20:53468831..53471072,3	MCF-7	breast:
5	chr20:53458657..53461544-chr20:53468848..53472413,4	MCF-7	breast:
6	chr20:53461969..53462960-chr20:53470530..53471462,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYP24A1-2	chr20:53470281-53472307	NONHSAT080421

No data

Variant related genes	Relation type
ENSG00000252089	Chromatin interaction

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1512065	0.86[EUR][1000 genomes]
rs2025128	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2025129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048504	0.88[EUR][1000 genomes]
rs2063519	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4811538	0.86[EUR][1000 genomes]
rs4811546	0.81[CEU][hapmap]
rs4811547	0.80[CEU][hapmap]
rs6014185	0.87[EUR][1000 genomes]
rs6023624	0.82[EUR][1000 genomes]
rs6023625	0.83[EUR][1000 genomes]
rs6023640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6023645	0.85[EUR][1000 genomes]
rs6064117	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6098273	0.92[ASN][1000 genomes]
rs6098274	0.92[ASN][1000 genomes]
rs6127294	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[ASN][1000 genomes]
rs912507	0.86[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	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
2	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6023649	ATP9A	cis	cerebellum	SCAN
rs6023649	PFDN4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53467600-53478000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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