Variant report

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52902315..52904046-chr20:52922393..52924271,2	MCF-7	breast:
2	chr20:52922776..52924284-chr20:52931074..52933006,2	MCF-7	breast:
3	chr20:52824550..52826498-chr20:52922860..52925164,2	MCF-7	breast:
4	chr20:52923632..52926364-chr20:52926650..52929482,4	MCF-7	breast:
5	chr20:52911450..52915662-chr20:52921093..52925920,4	MCF-7	breast:
6	chr20:52823568..52826063-chr20:52923324..52925181,2	MCF-7	breast:
7	chr20:52897965..52899622-chr20:52923358..52924887,2	MCF-7	breast:
8	chr20:52922402..52924055-chr20:52929439..52931142,2	MCF-7	breast:
9	chr20:52892335..52894745-chr20:52921772..52923928,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1293129	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1293131	0.88[ASN][1000 genomes]
rs1477736	0.81[CEU][hapmap]
rs1841861	0.82[ASN][1000 genomes]
rs28654312	0.88[ASN][1000 genomes]
rs4535116	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6013952	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs6013961	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013962	1.00[ASN][1000 genomes]
rs6013963	0.88[ASN][1000 genomes]
rs6023094	0.88[ASN][1000 genomes]
rs6023100	0.88[ASN][1000 genomes]
rs6023103	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023110	0.86[CHB][hapmap]
rs6023121	0.89[CHD][hapmap]
rs6091849	0.83[AFR][1000 genomes]
rs6097892	0.88[ASN][1000 genomes]
rs6097894	0.88[ASN][1000 genomes]
rs6123377	0.82[ASN][1000 genomes]
rs6127164	0.88[ASN][1000 genomes]
rs6127175	0.86[CHB][hapmap]
rs73914345	0.88[ASN][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	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	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6023101	GCNT7	cis	parietal	SCAN
rs6023101	LOC284751	cis	parietal	SCAN
rs6023101	RAE1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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