Variant report

Variant	rs1321465
Chromosome Location	chr20:53032161-53032162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53026253..53028850-chr20:53030160..53033071,3	MCF-7	breast:
2	chr20:53032153..53034811-chr9:37421058..37422667,2	MCF-7	breast:
3	chr20:53026209..53029176-chr20:53030755..53032487,3	MCF-7	breast:
4	chr20:53028966..53030621-chr20:53031320..53033737,2	MCF-7	breast:
5	chr20:53007873..53010357-chr20:53031258..53033220,2	MCF-7	breast:
6	chr20:53020134..53020896-chr20:53031789..53032367,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137106	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1007393	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1321464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358806	0.86[ASN][1000 genomes]
rs1358807	0.86[ASN][1000 genomes]
rs1407043	0.82[ASW][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs1590206	0.86[ASN][1000 genomes]
rs16999560	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs16999597	0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs17317237	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs2870329	0.86[ASN][1000 genomes]
rs35464585	0.82[ASN][1000 genomes]
rs6013997	0.85[JPT][hapmap]
rs6013999	0.82[AMR][1000 genomes]
rs6014003	0.82[AMR][1000 genomes]
rs6014004	0.87[AMR][1000 genomes]
rs6014011	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6014013	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023181	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs6023183	0.84[ASN][1000 genomes]
rs6023185	0.82[AMR][1000 genomes]
rs6023192	0.82[AMR][1000 genomes]
rs6023197	0.86[ASN][1000 genomes]
rs6023203	0.80[AMR][1000 genomes]
rs6023227	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097955	0.85[ASN][1000 genomes]
rs6097957	0.86[ASN][1000 genomes]
rs6097963	0.90[JPT][hapmap]
rs6097964	0.86[ASN][1000 genomes]
rs6097967	0.86[ASN][1000 genomes]
rs73147267	0.85[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1321465	ZNF217	cis	cerebellum	SCAN
rs1321465	KCNG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53032000-53033400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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