Variant report

Variant	rs56410772
Chromosome Location	chr21:17098219-17098220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr21:17098170-17098725	MCF-7	breast:	n/a	n/a
2	GATA3	chr21:17098207-17098678	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr21:17098112-17098978	MCF-7	breast:	n/a	n/a
4	GATA3	chr21:17098145-17098808	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17097568..17099854-chr21:17101138..17103471,3	K562	blood:
2	chr21:17097568..17099854-chr21:17100603..17103471,4	K562	blood:

Variant related genes	Relation type
USP25	TF binding region
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10482875	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10482876	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1543299	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241409	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17241416	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17241423	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17241430	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17241444	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17241460	0.84[AMR][1000 genomes]
rs17241481	0.84[AMR][1000 genomes]
rs17275511	0.84[ASN][1000 genomes]
rs17307120	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17307170	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17307176	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17307190	0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17307204	0.84[AMR][1000 genomes]
rs2205588	0.95[AMR][1000 genomes]
rs2242676	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242677	0.93[ASN][1000 genomes]
rs2242680	0.95[AMR][1000 genomes]
rs2242681	0.95[AMR][1000 genomes]
rs2404000	0.90[AMR][1000 genomes]
rs2823455	0.91[ASN][1000 genomes]
rs2823462	0.92[EUR][1000 genomes]
rs2823463	0.94[EUR][1000 genomes]
rs2823471	0.88[EUR][1000 genomes]
rs2823478	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2823491	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2823498	0.81[AMR][1000 genomes]
rs28627435	0.88[EUR][1000 genomes]
rs3787577	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55806628	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56299770	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56333224	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56666611	0.89[EUR][1000 genomes]
rs57733106	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57737796	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59084861	0.95[AMR][1000 genomes]
rs59420372	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60191002	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60360638	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60529604	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6517675	0.82[ASN][1000 genomes]
rs7277807	0.95[EUR][1000 genomes]
rs7278428	0.84[EUR][1000 genomes]
rs7281511	0.82[ASN][1000 genomes]
rs7282314	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7283764	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73181987	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73346766	0.82[ASN][1000 genomes]
rs73346769	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73355479	0.92[EUR][1000 genomes]
rs73357260	0.89[EUR][1000 genomes]
rs8133079	0.84[AMR][1000 genomes]
rs9976815	0.91[ASN][1000 genomes]
rs9983542	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv2830057	chr21:16960590-17113148	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1060139	chr21:17057044-17100275	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17096800-17101800	Weak transcription	Placenta	Placenta
2	chr21:17097600-17101600	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links