Variant report

Variant	rs228477
Chromosome Location	chr1:79698076-79698077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11162676	0.91[ASN][1000 genomes]
rs11162677	0.91[ASN][1000 genomes]
rs12064196	0.91[ASN][1000 genomes]
rs12093328	0.91[ASN][1000 genomes]
rs12401629	0.91[ASN][1000 genomes]
rs1331717	0.91[ASN][1000 genomes]
rs170611	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170614	0.85[EUR][1000 genomes]
rs17102981	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs172926	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs183458	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs228466	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228467	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228468	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228472	0.84[AMR][1000 genomes]
rs228474	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228480	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228482	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228483	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228484	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228485	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228486	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228487	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228489	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228494	0.86[EUR][1000 genomes]
rs228495	0.86[EUR][1000 genomes]
rs228496	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs228497	0.80[EUR][1000 genomes]
rs228499	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228500	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228502	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228506	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228508	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228510	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs228511	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228512	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228514	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228515	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs228516	0.86[EUR][1000 genomes]
rs228517	0.87[EUR][1000 genomes]
rs228518	0.87[EUR][1000 genomes]
rs228519	0.87[EUR][1000 genomes]
rs228522	0.87[EUR][1000 genomes]
rs228523	0.86[EUR][1000 genomes]
rs228534	0.85[EUR][1000 genomes]
rs228535	0.85[EUR][1000 genomes]
rs228537	0.85[EUR][1000 genomes]
rs228541	0.84[EUR][1000 genomes]
rs228542	0.84[EUR][1000 genomes]
rs35764284	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs368460	0.82[AMR][1000 genomes]
rs393486	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs417181	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418641	0.84[AMR][1000 genomes]
rs427551	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428585	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650312	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650316	0.91[ASN][1000 genomes]
rs4650402	0.84[AMR][1000 genomes]
rs4650403	0.84[AMR][1000 genomes]
rs61766097	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6424644	0.84[AMR][1000 genomes]
rs6424645	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674681	0.84[AMR][1000 genomes]
rs6681555	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7520891	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551723	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7553133	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830326	chr1:79573379-79735667	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv871182	chr1:79614989-79822735	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv999471	chr1:79650363-79774433	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79696000-79698200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:79697400-79698400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:79697400-79698800	Enhancers	Placenta	Placenta
4	chr1:79697600-79699600	Enhancers	Hela-S3	cervix
5	chr1:79697800-79701000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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