Variant report

Variant	rs16999597
Chromosome Location	chr20:53019533-53019534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53019454..53021882-chr20:53023478..53026443,2	MCF-7	breast:
2	chr20:53016400..53017924-chr20:53017954..53020403,2	MCF-7	breast:
3	chr20:53018931..53021267-chr9:130211342..130214150,2	MCF-7	breast:
4	chr20:52823542..52826104-chr20:53017134..53020840,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000148356	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1007393	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1014808	0.84[ASN][1000 genomes]
rs1321464	0.90[JPT][hapmap]
rs1321465	0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs1321468	0.90[JPT][hapmap]
rs1358806	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1358807	0.91[ASN][1000 genomes]
rs1407043	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1590206	0.92[ASN][1000 genomes]
rs1923118	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28406117	0.84[ASN][1000 genomes]
rs28429972	0.85[ASN][1000 genomes]
rs2870329	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56881371	0.88[ASN][1000 genomes]
rs59924072	0.85[ASN][1000 genomes]
rs6013987	0.84[ASN][1000 genomes]
rs6013989	0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs6013997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6013999	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6014003	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6014004	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6014005	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6014011	0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs6014013	0.81[AMR][1000 genomes]
rs6023153	0.88[ASN][1000 genomes]
rs6023154	0.88[ASN][1000 genomes]
rs6023155	0.89[ASN][1000 genomes]
rs6023156	0.89[ASN][1000 genomes]
rs6023158	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs6023163	0.85[ASN][1000 genomes]
rs6023164	0.85[ASN][1000 genomes]
rs6023178	0.85[ASN][1000 genomes]
rs6023179	0.85[ASN][1000 genomes]
rs6023180	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6023181	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]
rs6023183	0.89[ASN][1000 genomes]
rs6023185	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6023189	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023192	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023193	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023197	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6023203	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023227	0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs6097934	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs6097938	0.84[ASN][1000 genomes]
rs6097939	0.88[ASN][1000 genomes]
rs6097940	0.87[ASN][1000 genomes]
rs6097941	0.87[ASN][1000 genomes]
rs6097945	0.83[ASN][1000 genomes]
rs6097946	0.83[ASN][1000 genomes]
rs6097955	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097957	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097963	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	0.84[ASN][1000 genomes]
rs73624108	0.85[ASN][1000 genomes]
rs73624110	0.85[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
rs16999597	ZNF217	cis	cerebellum	SCAN

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

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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