Variant report

Variant	rs28563055
Chromosome Location	chr19:52742963-52742964
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	chr19:52691100..52693338-chr19:52742359..52744516,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105568	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10402209	0.94[ASN][1000 genomes]
rs10402638	0.94[ASN][1000 genomes]
rs10403283	0.96[ASN][1000 genomes]
rs10403311	0.86[ASN][1000 genomes]
rs10403806	0.94[ASN][1000 genomes]
rs10404437	0.94[ASN][1000 genomes]
rs10407063	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10407502	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10408119	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10411211	0.96[ASN][1000 genomes]
rs10412110	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10412196	0.90[ASN][1000 genomes]
rs10413012	0.96[ASN][1000 genomes]
rs10414083	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10414197	0.94[ASN][1000 genomes]
rs10414423	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10414536	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10414852	0.94[ASN][1000 genomes]
rs10416785	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10417033	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10417253	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10418666	0.82[ASN][1000 genomes]
rs10420207	0.84[ASN][1000 genomes]
rs10420560	0.94[ASN][1000 genomes]
rs10421589	0.86[ASN][1000 genomes]
rs10422838	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10423125	0.86[ASN][1000 genomes]
rs10425135	0.94[ASN][1000 genomes]
rs10426002	0.96[ASN][1000 genomes]
rs10426786	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16983598	0.94[ASN][1000 genomes]
rs16983601	0.94[ASN][1000 genomes]
rs16983603	0.96[ASN][1000 genomes]
rs16983610	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16983619	0.85[AFR][1000 genomes]
rs16983648	0.82[AFR][1000 genomes]
rs2115074	0.98[ASN][1000 genomes]
rs28444225	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4327163	0.85[AFR][1000 genomes]
rs55751302	0.96[ASN][1000 genomes]
rs55871532	0.96[ASN][1000 genomes]
rs57102373	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs57370252	0.85[AFR][1000 genomes]
rs60063830	0.96[ASN][1000 genomes]
rs60307688	0.85[AFR][1000 genomes]
rs6509628	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6509629	0.85[AFR][1000 genomes]
rs7249460	0.96[ASN][1000 genomes]
rs7250109	0.85[AFR][1000 genomes]
rs7255058	0.92[ASN][1000 genomes]
rs7255677	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7255737	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256125	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256216	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7256300	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256312	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256719	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259175	0.90[ASN][1000 genomes]
rs73935052	0.94[ASN][1000 genomes]
rs73935053	0.96[ASN][1000 genomes]
rs73935058	0.85[AFR][1000 genomes]
rs8100048	0.92[ASN][1000 genomes]
rs8105432	0.94[ASN][1000 genomes]
rs8106544	0.88[ASN][1000 genomes]
rs8108636	0.94[ASN][1000 genomes]
rs8109512	0.94[ASN][1000 genomes]
rs8110857	0.94[ASN][1000 genomes]
rs8110881	0.94[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52733200-52759600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:52734400-52751600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr19:52734600-52743800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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