Variant report

Variant	rs6778020
Chromosome Location	chr3:23619213-23619214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11914576	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919065	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926217	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486880	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12637722	0.86[EUR][1000 genomes]
rs17013412	0.86[ASN][1000 genomes]
rs1826847	0.87[ASN][1000 genomes]
rs2133330	0.95[ASN][1000 genomes]
rs34710747	0.92[ASN][1000 genomes]
rs35169377	0.88[AFR][1000 genomes]
rs4642064	0.96[ASN][1000 genomes]
rs55666330	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55732421	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55779138	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56964757	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57172051	0.90[ASN][1000 genomes]
rs57258152	0.94[ASN][1000 genomes]
rs57278918	0.95[ASN][1000 genomes]
rs57604595	0.90[ASN][1000 genomes]
rs57801020	0.92[ASN][1000 genomes]
rs58068931	0.95[ASN][1000 genomes]
rs58486254	0.93[ASN][1000 genomes]
rs59580282	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60221455	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60759404	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61363919	0.80[EUR][1000 genomes]
rs6550765	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs66900833	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6775891	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6775907	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6781388	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6782079	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6799118	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6802488	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6807788	0.87[ASN][1000 genomes]
rs73043636	0.95[ASN][1000 genomes]
rs73043687	0.94[ASN][1000 genomes]
rs73045615	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73045617	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73045660	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73049414	0.87[EUR][1000 genomes]
rs7609845	0.88[AFR][1000 genomes]
rs7610906	0.86[ASN][1000 genomes]
rs7620266	0.95[ASN][1000 genomes]
rs7624174	0.90[AFR][1000 genomes]
rs7628135	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7628949	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7631705	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7632814	0.94[ASN][1000 genomes]
rs7640458	0.92[ASN][1000 genomes]
rs7643270	0.95[ASN][1000 genomes]
rs9812300	0.92[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	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23606000-23643000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:23607000-23640400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:23608600-23634400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:23609400-23637800	Weak transcription	HSMMtube	muscle
5	chr3:23617200-23635600	Weak transcription	Fetal Thymus	thymus
6	chr3:23617400-23623400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:23617600-23621600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:23618400-23619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:23618400-23621000	Weak transcription	Hela-S3	cervix
10	chr3:23618400-23621400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:23618800-23619400	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr3:23619200-23621000	Weak transcription	A549	lung

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