Variant report

Variant	rs6549880
Chromosome Location	chr3:28745955-28745956
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10510614	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11718080	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925269	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1381393	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17021806	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17021860	0.81[EUR][1000 genomes]
rs4258916	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4315650	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4530489	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4624524	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680775	0.85[AFR][1000 genomes]
rs56212205	0.81[EUR][1000 genomes]
rs56299573	0.81[EUR][1000 genomes]
rs59333989	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61287529	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6549871	0.96[ASN][1000 genomes]
rs6549874	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67946732	0.81[EUR][1000 genomes]
rs6804117	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73054642	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73054682	0.83[ASN][1000 genomes]
rs73065090	0.81[ASN][1000 genomes]
rs9875435	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv916364	chr3:28468275-29146280	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1001920	chr3:28711075-28788920	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28745000-28746200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr3:28745200-28746600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:28745200-28746600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr3:28745200-28746600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr3:28745400-28746000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:28745400-28746000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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