Variant report

Variant	rs6098064
Chromosome Location	chr20:53160179-53160180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53156431..53159299-chr20:53159745..53162526,2	MCF-7	breast:
2	chr20:53158565..53163438-chr20:53165298..53171299,6	MCF-7	breast:
3	chr20:53151757..53155024-chr20:53157486..53161432,6	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10485786	0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs16999731	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16999732	1.00[JPT][hapmap]
rs16999736	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs16999764	0.85[CHD][hapmap]
rs16999772	0.84[MEX][hapmap];0.88[TSI][hapmap]
rs2426521	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2426522	0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2426525	0.98[ASN][1000 genomes]
rs2426526	0.96[ASN][1000 genomes]
rs2426529	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2426530	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2426531	1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs2426535	1.00[ASN][1000 genomes]
rs2426536	0.93[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57402636	1.00[ASN][1000 genomes]
rs6014049	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6014050	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs6014052	0.88[TSI][hapmap]
rs6014055	0.88[TSI][hapmap]
rs6014056	0.87[TSI][hapmap]
rs6014057	0.88[TSI][hapmap]
rs6023341	0.81[EUR][1000 genomes]
rs6023342	0.81[EUR][1000 genomes]
rs6023344	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023357	0.88[TSI][hapmap]
rs6091909	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6098044	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs6098074	0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67854575	0.81[EUR][1000 genomes]
rs726770	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7272302	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7274532	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276924	0.98[ASN][1000 genomes]
rs8117905	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8126261	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs974461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917433	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6098064	RAE1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53153000-53161800	Weak transcription	Osteobl	bone
2	chr20:53158800-53161200	Weak transcription	Fetal Brain Male	brain

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