Variant report

Variant	rs2806399
Chromosome Location	chr1:58617269-58617270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10889085	0.81[EUR][1000 genomes]
rs10889086	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11207174	1.00[CEU][hapmap]
rs12401924	1.00[CEU][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs1776183	0.99[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981196	0.91[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3850537	0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs471080	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs482637	0.83[CEU][hapmap]
rs488944	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs501582	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs502534	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs507981	0.85[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs538348	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544369	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs548745	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572888	0.91[CEU][hapmap]
rs593257	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60404864	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs625994	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587803	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs677451	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7524008	1.00[CEU][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2806399	ACOT11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58616000-58617600	Weak transcription	Liver	Liver

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