Variant report

Variant	rs56945578
Chromosome Location	chr3:145983104-145983105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs13071899	0.81[AFR][1000 genomes]
rs13072399	0.90[AFR][1000 genomes]
rs13097291	0.82[AFR][1000 genomes]
rs16858173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16858176	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16858179	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41358845	1.00[EUR][1000 genomes]
rs41537446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56364069	0.90[EUR][1000 genomes]
rs57016931	1.00[EUR][1000 genomes]
rs57202132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57555021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57702664	1.00[EUR][1000 genomes]
rs57852021	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58284373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58434679	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58523990	1.00[EUR][1000 genomes]
rs59001257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59060080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59125030	1.00[EUR][1000 genomes]
rs59201889	1.00[EUR][1000 genomes]
rs59202860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59652731	1.00[EUR][1000 genomes]
rs60028092	1.00[EUR][1000 genomes]
rs60271422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60489907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60843942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60922478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61440265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440427	1.00[EUR][1000 genomes]
rs6765013	1.00[EUR][1000 genomes]
rs6766725	0.90[EUR][1000 genomes]
rs6767570	1.00[EUR][1000 genomes]
rs6777637	1.00[EUR][1000 genomes]
rs6777974	1.00[EUR][1000 genomes]
rs72991486	0.90[EUR][1000 genomes]
rs72991490	0.90[EUR][1000 genomes]
rs72991492	0.90[EUR][1000 genomes]
rs72991494	0.90[EUR][1000 genomes]
rs72992903	1.00[EUR][1000 genomes]
rs72992908	1.00[EUR][1000 genomes]
rs72992924	1.00[EUR][1000 genomes]
rs72992931	1.00[EUR][1000 genomes]
rs72992934	1.00[EUR][1000 genomes]
rs72992963	1.00[EUR][1000 genomes]
rs72992964	1.00[EUR][1000 genomes]
rs72992966	1.00[EUR][1000 genomes]
rs72992968	1.00[EUR][1000 genomes]
rs72992969	1.00[EUR][1000 genomes]
rs72992975	1.00[EUR][1000 genomes]
rs72992981	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72992986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72992988	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72992989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72993002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995010	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995014	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995019	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995022	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995025	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72995034	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72999169	1.00[EUR][1000 genomes]
rs72999182	1.00[EUR][1000 genomes]
rs72999189	1.00[EUR][1000 genomes]
rs72999197	1.00[EUR][1000 genomes]
rs73001103	1.00[EUR][1000 genomes]
rs73001107	1.00[EUR][1000 genomes]
rs73001112	1.00[EUR][1000 genomes]
rs73001132	1.00[EUR][1000 genomes]
rs73001133	1.00[EUR][1000 genomes]
rs73865394	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73867504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73867507	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73867511	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73867513	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73867518	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73867520	1.00[EUR][1000 genomes]
rs73867521	1.00[EUR][1000 genomes]
rs73867523	1.00[EUR][1000 genomes]
rs7610563	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629318	1.00[EUR][1000 genomes]
rs7630137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630230	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7632298	1.00[EUR][1000 genomes]
rs7642529	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7650158	1.00[EUR][1000 genomes]
rs7650651	1.00[EUR][1000 genomes]
rs7651598	1.00[EUR][1000 genomes]
rs7651977	1.00[EUR][1000 genomes]
rs7652262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652376	0.90[AFR][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	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv998388	chr3:145960954-146087749	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145976200-145983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:145977000-145984600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:145982200-145985400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:145982800-145983200	Enhancers	Hela-S3	cervix
5	chr3:145982800-145983600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:145982800-145984600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:145982800-145984600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:145982800-145984800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:145983000-145983600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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