Variant report

Variant	rs2152019
Chromosome Location	chr10:28156285-28156286
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10826357	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10826358	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10826359	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10826360	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10826362	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10826363	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10826364	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10826365	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11006756	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11006759	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11006760	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11006761	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11006762	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11006765	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11006766	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11006767	0.86[EUR][1000 genomes]
rs11492473	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11595783	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11816757	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12358199	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12358283	0.85[EUR][1000 genomes]
rs1334719	0.95[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1413772	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1832005	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2065690	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2152018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2184418	0.87[EUR][1000 genomes]
rs2368266	0.84[CHD][hapmap];0.85[GIH][hapmap]
rs2368269	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2368271	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4749266	0.81[CEU][hapmap]
rs4749267	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4749273	0.95[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs4749275	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4749276	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4749277	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4749278	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4749279	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4749280	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6481484	0.84[CHD][hapmap];0.88[GIH][hapmap]
rs6481485	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs7070860	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7076149	0.88[ASN][1000 genomes]
rs7077304	0.89[MKK][hapmap];0.80[TSI][hapmap]
rs7077472	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7078534	0.84[CHD][hapmap];0.88[GIH][hapmap]
rs7090390	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7094167	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7094542	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7095239	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7095692	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7096964	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7099583	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7099871	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7099876	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7100494	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7897889	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs880706	0.95[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs880707	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs880708	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs915175	0.86[CHD][hapmap];0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831813	chr10:28017606-28200651	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv971859	chr10:28070066-28271252	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv550283	chr10:28144330-28167326	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2152019	ZNF79	trans	cerebellum	SCAN
rs2152019	KIAA1217	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28121000-28158600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:28154800-28158400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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