Variant report

Variant	rs58548979
Chromosome Location	chr3:51143844-51143845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs17051747	1.00[EUR][1000 genomes]
rs17051755	1.00[EUR][1000 genomes]
rs55640023	1.00[EUR][1000 genomes]
rs55694933	1.00[EUR][1000 genomes]
rs55699461	1.00[EUR][1000 genomes]
rs55708856	1.00[EUR][1000 genomes]
rs56037427	1.00[EUR][1000 genomes]
rs56254449	1.00[EUR][1000 genomes]
rs56870664	1.00[EUR][1000 genomes]
rs56890263	1.00[EUR][1000 genomes]
rs56940802	1.00[EUR][1000 genomes]
rs56962519	1.00[EUR][1000 genomes]
rs57376071	1.00[EUR][1000 genomes]
rs57723217	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57742040	1.00[EUR][1000 genomes]
rs58225351	1.00[EUR][1000 genomes]
rs58236908	1.00[EUR][1000 genomes]
rs58293845	1.00[EUR][1000 genomes]
rs58803807	1.00[EUR][1000 genomes]
rs59019902	1.00[EUR][1000 genomes]
rs59557845	1.00[EUR][1000 genomes]
rs59599274	1.00[EUR][1000 genomes]
rs59652730	1.00[EUR][1000 genomes]
rs59794491	1.00[EUR][1000 genomes]
rs60166061	1.00[EUR][1000 genomes]
rs60862896	1.00[EUR][1000 genomes]
rs60973580	1.00[EUR][1000 genomes]
rs61174735	1.00[EUR][1000 genomes]
rs61337570	1.00[EUR][1000 genomes]
rs61526358	1.00[EUR][1000 genomes]
rs61570923	1.00[EUR][1000 genomes]
rs6781959	1.00[EUR][1000 genomes]
rs6799213	1.00[EUR][1000 genomes]
rs6804101	1.00[EUR][1000 genomes]
rs6805545	1.00[EUR][1000 genomes]
rs73833977	1.00[EUR][1000 genomes]
rs73833978	1.00[EUR][1000 genomes]
rs73833980	1.00[EUR][1000 genomes]
rs73833981	1.00[EUR][1000 genomes]
rs73833982	1.00[EUR][1000 genomes]
rs73833985	1.00[EUR][1000 genomes]
rs73833986	1.00[EUR][1000 genomes]
rs73833987	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833989	1.00[EUR][1000 genomes]
rs73833990	1.00[EUR][1000 genomes]
rs73833991	1.00[EUR][1000 genomes]
rs73833992	1.00[EUR][1000 genomes]
rs73833993	1.00[EUR][1000 genomes]
rs73833996	1.00[EUR][1000 genomes]
rs73837406	1.00[EUR][1000 genomes]
rs73837420	1.00[EUR][1000 genomes]
rs73837421	1.00[EUR][1000 genomes]
rs73837422	1.00[EUR][1000 genomes]
rs73837423	1.00[EUR][1000 genomes]
rs73837425	1.00[EUR][1000 genomes]
rs73837428	1.00[EUR][1000 genomes]
rs73837431	1.00[EUR][1000 genomes]
rs73837432	1.00[EUR][1000 genomes]
rs73837433	1.00[EUR][1000 genomes]
rs73837434	1.00[EUR][1000 genomes]
rs7630259	1.00[EUR][1000 genomes]
rs7635095	1.00[EUR][1000 genomes]
rs7642077	1.00[EUR][1000 genomes]
rs9311462	1.00[EUR][1000 genomes]
rs9990213	1.00[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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv3447639	chr3:51129523-51158383	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51121000-51145200	Weak transcription	Fetal Brain Male	brain
2	chr3:51142000-51145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:51142600-51144200	Strong transcription	Brain Inferior Temporal Lobe	brain
4	chr3:51143000-51144000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:51143000-51144000	Strong transcription	Brain Hippocampus Middle	brain
6	chr3:51143000-51144200	Strong transcription	Brain Germinal Matrix	brain
7	chr3:51143000-51144200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:51143000-51144400	Strong transcription	Brain Angular Gyrus	brain
9	chr3:51143000-51144800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:51143000-51145000	ZNF genes & repeats	Fetal Brain Female	brain
11	chr3:51143200-51144200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:51143200-51144400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:51143200-51144400	Strong transcription	Brain Substantia Nigra	brain
14	chr3:51143200-51144600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:51143400-51144600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:51143600-51144000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:51143600-51144200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr3:51143800-51144000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr3:51143800-51144000	Strong transcription	Brain Cingulate Gyrus	brain
20	chr3:51143800-51144200	Strong transcription	Brain Anterior Caudate	brain
21	chr3:51143800-51144400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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