Variant report

Variant	rs9859898
Chromosome Location	chr3:54382247-54382248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12632182	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12633531	1.00[CHB][hapmap]
rs13314582	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13319005	1.00[YRI][hapmap]
rs28550373	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28623181	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6414576	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs9809130	1.00[YRI][hapmap]
rs9816445	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9817852	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9818719	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9822780	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9844238	1.00[YRI][hapmap]
rs9849141	1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9863977	1.00[YRI][hapmap]
rs9864089	1.00[YRI][hapmap]
rs9874563	1.00[YRI][hapmap]
rs9875018	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs9876334	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs9877208	1.00[YRI][hapmap]

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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54377200-54383200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:54377800-54383200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:54378400-54383200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:54378800-54389000	Weak transcription	Psoas Muscle	Psoas
5	chr3:54379200-54383200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:54380000-54383000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:54380000-54383200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:54380000-54391200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:54380200-54387200	Weak transcription	Ovary	ovary
10	chr3:54380400-54382400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:54381200-54383200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:54381200-54383200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:54381200-54383200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:54381200-54383400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:54381800-54382800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:54382000-54384800	Enhancers	Hela-S3	cervix
17	chr3:54382200-54382400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:54382200-54384200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:54382200-54384800	Enhancers	Fetal Lung	lung

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