Variant report

Variant	rs28379669
Chromosome Location	chr3:19119949-19119950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1449942	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1579992	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28532618	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28828139	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4246663	0.84[EUR][1000 genomes]
rs4408886	0.84[EUR][1000 genomes]
rs4455337	0.96[EUR][1000 genomes]
rs4491922	0.84[EUR][1000 genomes]
rs4493455	0.84[EUR][1000 genomes]
rs4510398	0.84[EUR][1000 genomes]
rs4973720	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55832040	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6419849	0.81[EUR][1000 genomes]
rs6550856	0.83[EUR][1000 genomes]
rs6550868	0.84[EUR][1000 genomes]
rs6550872	0.84[EUR][1000 genomes]
rs6550873	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6550888	0.90[EUR][1000 genomes]
rs6550937	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6800676	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6802959	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6807205	0.84[EUR][1000 genomes]
rs73048510	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7373868	0.84[EUR][1000 genomes]
rs7374105	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7374279	0.84[EUR][1000 genomes]
rs7374571	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7426697	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7428855	0.84[EUR][1000 genomes]
rs7428897	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7430996	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7433155	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7433351	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7612947	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7633015	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9310591	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820260	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9823816	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9831536	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9832066	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832959	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9836382	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9837132	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863039	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9863583	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9866954	0.81[AMR][1000 genomes];0.87[EUR][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	nsv517847	chr3:18845347-19483695	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19116800-19125000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:19117000-19120200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:19117400-19120600	Enhancers	Brain Germinal Matrix	brain
4	chr3:19117600-19120000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:19117800-19120200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:19119200-19120400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr3:19119400-19120400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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