Variant report

Variant	rs6858759
Chromosome Location	chr4:20952445-20952446
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10011942	0.81[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs10461094	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11727035	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13129855	0.87[JPT][hapmap]
rs13151383	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1347385	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1352796	0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs1388326	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs1434943	0.84[TSI][hapmap]
rs1434946	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1434947	0.87[EUR][1000 genomes]
rs1434950	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1491356	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1491357	0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs1491361	1.00[JPT][hapmap]
rs1491369	0.87[JPT][hapmap]
rs1565534	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1836520	0.96[ASN][1000 genomes]
rs1865444	0.93[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4395501	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4441750	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696968	0.87[ASN][1000 genomes]
rs4697196	0.90[ASN][1000 genomes]
rs6447998	0.93[JPT][hapmap]
rs6447999	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap]
rs6448003	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6448004	0.93[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6811024	0.82[ASW][hapmap];0.88[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs6832672	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs6836783	0.90[ASN][1000 genomes]
rs6843757	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs7677635	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7677781	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7690016	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs980276	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv829877	chr4:20847465-20992544	Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6858759	PPARGC1A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20945600-20959600	Weak transcription	Colon Smooth Muscle	Colon

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