Variant report

Variant	rs1500009
Chromosome Location	chr3:28923882-28923883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11709945	1.00[ASN][1000 genomes]
rs11713577	0.97[ASN][1000 genomes]
rs11717153	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715148	1.00[ASN][1000 genomes]
rs13320621	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1353923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353928	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353929	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353930	0.96[EUR][1000 genomes]
rs1392299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392302	0.96[EUR][1000 genomes]
rs1392303	1.00[ASN][1000 genomes]
rs1500008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500013	0.96[EUR][1000 genomes]
rs17654965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875128	0.93[EUR][1000 genomes]
rs1909600	0.91[EUR][1000 genomes]
rs2201985	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221154	0.89[EUR][1000 genomes]
rs3856683	0.88[EUR][1000 genomes]
rs4270468	0.86[EUR][1000 genomes]
rs4490310	0.83[EUR][1000 genomes]
rs6549894	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6549897	0.88[EUR][1000 genomes]
rs6764257	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773079	0.88[EUR][1000 genomes]
rs6799656	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6805815	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616032	0.91[EUR][1000 genomes]
rs7619942	0.96[EUR][1000 genomes]
rs7626502	0.95[EUR][1000 genomes]
rs7637007	0.95[EUR][1000 genomes]
rs7639242	1.00[ASN][1000 genomes]
rs9816337	0.93[EUR][1000 genomes]
rs9820080	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833538	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837208	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846314	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852364	0.86[EUR][1000 genomes]
rs9859416	0.84[EUR][1000 genomes]
rs9862610	0.87[EUR][1000 genomes]

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	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
2	nsv590011	chr3:28780713-29044437	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv876652	chr3:28811329-28947691	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv876653	chr3:28819123-29366164	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv876654	chr3:28882980-29105082	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1008133	chr3:28910310-28950047	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28903800-28928200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:28922600-28924000	Enhancers	NHDF-Ad	bronchial
3	chr3:28923600-28924000	Enhancers	Skeletal Muscle Male	skeletal muscle

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