Variant report

No.	Distal block	Cell Line	Cell type
1	chr20:53419453..53421420-chr20:53458481..53461385,2	MCF-7	breast:
2	chr20:53458659..53460997-chr21:40686277..40688957,2	MCF-7	breast:
3	chr20:53456314..53458987-chr20:53459309..53462293,2	MCF-7	breast:
4	chr20:53458657..53461544-chr20:53468848..53472413,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255568	Chromatin interaction
ENSG00000238141	Chromatin interaction

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1512065	0.91[EUR][1000 genomes]
rs2025128	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2025129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048504	0.89[EUR][1000 genomes]
rs2063519	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063520	0.90[YRI][hapmap]
rs2063521	0.87[AFR][1000 genomes]
rs4811538	0.91[EUR][1000 genomes]
rs4811546	0.81[CEU][hapmap]
rs4811547	0.82[TSI][hapmap]
rs6014185	0.88[EUR][1000 genomes]
rs6023624	0.88[EUR][1000 genomes]
rs6023625	0.88[EUR][1000 genomes]
rs6023645	0.89[EUR][1000 genomes]
rs6023649	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]
rs6064117	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6098273	0.98[ASN][1000 genomes]
rs6098274	0.98[ASN][1000 genomes]
rs6127294	1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[ASN][1000 genomes]
rs912507	0.88[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
rs6023640	PFDN4	cis	cerebellum	SCAN
rs6023640	ATP9A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53458400-53459200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

Quick Search: