Variant report

Variant	rs1321468
Chromosome Location	chr20:53029021-53029022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53004386..53007299-chr20:53027791..53029630,2	MCF-7	breast:
2	chr20:53028096..53030444-chr20:53043219..53045121,2	MCF-7	breast:
3	chr20:53028712..53031631-chr20:53050786..53053214,2	MCF-7	breast:
4	chr20:53028966..53030621-chr20:53031320..53033737,2	MCF-7	breast:
5	chr20:53024067..53025831-chr20:53028863..53030621,2	MCF-7	breast:
6	chr2:54342491..54344563-chr20:53027909..53030153,2	MCF-7	breast:
7	chr20:53026209..53029176-chr20:53030755..53032487,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1007393	0.91[ASN][1000 genomes]
rs1321464	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1321465	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	0.85[JPT][hapmap]
rs1539515	0.81[EUR][1000 genomes]
rs1590206	0.87[ASN][1000 genomes]
rs16999560	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs16999597	0.90[JPT][hapmap]
rs17317237	1.00[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs2126677	0.83[EUR][1000 genomes]
rs2870329	0.86[ASN][1000 genomes]
rs35464585	0.82[ASN][1000 genomes]
rs55865213	0.83[EUR][1000 genomes]
rs56339826	0.83[EUR][1000 genomes]
rs6013997	0.85[JPT][hapmap]
rs6014005	0.84[AMR][1000 genomes]
rs6014011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6014013	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6023178	0.80[ASN][1000 genomes]
rs6023179	0.80[ASN][1000 genomes]
rs6023181	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs6023183	0.84[ASN][1000 genomes]
rs6023193	0.80[AMR][1000 genomes]
rs6023197	0.86[ASN][1000 genomes]
rs6023227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6091858	0.81[EUR][1000 genomes]
rs6091860	0.83[EUR][1000 genomes]
rs6097942	0.81[EUR][1000 genomes]
rs6097943	0.81[EUR][1000 genomes]
rs6097950	0.83[EUR][1000 genomes]
rs6097955	0.86[ASN][1000 genomes]
rs6097957	0.86[ASN][1000 genomes]
rs6097963	0.90[JPT][hapmap]
rs6097964	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6097967	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73143321	0.83[EUR][1000 genomes]
rs73143323	0.83[EUR][1000 genomes]
rs73145242	0.83[EUR][1000 genomes]
rs73145250	0.83[EUR][1000 genomes]
rs73145257	0.83[EUR][1000 genomes]
rs73145263	0.83[EUR][1000 genomes]
rs73145273	0.83[EUR][1000 genomes]
rs73145277	0.83[EUR][1000 genomes]
rs73147267	0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1321468	ZNF217	cis	cerebellum	SCAN
rs1321468	TSHZ2	cis	parietal	SCAN
rs1321468	KCNG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53027000-53031400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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