Variant report

Variant	rs6023181
Chromosome Location	chr20:53001615-53001616
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52882145..52883756-chr20:53001250..53003874,2	MCF-7	breast:
2	chr20:53000318..53001983-chr20:53203861..53206076,2	MCF-7	breast:
3	chr17:57923666..57925669-chr20:53000512..53003012,2	MCF-7	breast:
4	chr20:52994488..52996309-chr20:53000177..53002729,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201524	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1007393	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1014808	0.99[ASN][1000 genomes]
rs1321464	0.82[CHB][hapmap]
rs1321465	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs1321468	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs1358806	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1358807	0.93[ASN][1000 genomes]
rs1407043	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1590206	0.92[ASN][1000 genomes]
rs16999597	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1841860	0.90[ASN][1000 genomes]
rs1923118	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2126676	0.92[ASN][1000 genomes]
rs28406117	0.83[ASN][1000 genomes]
rs28429972	0.84[ASN][1000 genomes]
rs2870329	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59924072	0.84[ASN][1000 genomes]
rs6013987	0.83[ASN][1000 genomes]
rs6013989	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6013997	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6013999	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6014003	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6014004	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6014005	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6014011	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs6023155	0.81[ASN][1000 genomes]
rs6023156	0.81[ASN][1000 genomes]
rs6023158	0.81[ASN][1000 genomes]
rs6023163	0.84[ASN][1000 genomes]
rs6023164	0.84[ASN][1000 genomes]
rs6023178	1.00[ASN][1000 genomes]
rs6023179	1.00[ASN][1000 genomes]
rs6023180	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6023183	0.95[ASN][1000 genomes]
rs6023185	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6023189	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6023192	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6023193	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6023197	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6023203	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6023227	0.82[CHB][hapmap]
rs6091856	0.91[ASN][1000 genomes]
rs6097939	0.80[ASN][1000 genomes]
rs6097945	0.82[ASN][1000 genomes]
rs6097946	0.82[ASN][1000 genomes]
rs6097955	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6097957	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6097963	0.85[ASN][1000 genomes]
rs6097964	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6097967	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73624107	0.83[ASN][1000 genomes]
rs73624108	0.84[ASN][1000 genomes]
rs73624110	0.84[ASN][1000 genomes]
rs793033	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6023181	ZNF217	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53001200-53002600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:53001600-53001800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links