Variant report

Variant	rs1841371
Chromosome Location	chr4:21491001-21491002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1013568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805225	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs11732183	0.83[EUR][1000 genomes]
rs11736408	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs11737456	0.86[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs12507996	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs12640010	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1460494	0.82[MEX][hapmap]
rs17466482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1841372	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976299	0.86[CHB][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs1976300	0.86[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs1993683	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2322965	0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2322966	0.91[ASN][1000 genomes]
rs4552441	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6827581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842233	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs6847007	0.86[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7688716	0.86[CHD][hapmap];1.00[JPT][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	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
2	nsv829879	chr4:21418568-21611002	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv998481	chr4:21421945-21608805	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv527163	chr4:21490361-21494981	Strong transcription Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1841371	PPARGC1A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21487600-21492600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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