Variant report

Variant	rs9548000
Chromosome Location	chr13:38224053-38224054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1006416	1.00[JPT][hapmap]
rs1028728	1.00[JPT][hapmap]
rs11147662	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11619443	1.00[JPT][hapmap]
rs11843893	0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17197908	1.00[JPT][hapmap]
rs28373781	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28646275	0.83[EUR][1000 genomes]
rs4432141	1.00[JPT][hapmap]
rs56312513	0.83[EUR][1000 genomes]
rs56361602	0.85[ASN][1000 genomes]
rs59082193	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7321585	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7321872	0.95[CEU][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs7330679	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532093	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9532095	0.91[CEU][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs9547958	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9547964	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9547965	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs9547991	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9547992	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9547994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9547996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9547997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9547998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs9547999	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548003	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548008	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548026	0.95[CEU][hapmap];0.82[TSI][hapmap]

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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr13:38211400-38275600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr13:38219600-38230600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:38219800-38224400	Weak transcription	Fetal Brain Male	brain
4	chr13:38220400-38224200	Weak transcription	Placenta	Placenta
5	chr13:38221600-38226600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:38221600-38226800	Weak transcription	NH-A	brain
7	chr13:38221600-38228200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:38221600-38228200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:38221600-38239600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr13:38221800-38231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:38221800-38233200	Weak transcription	Ovary	ovary
12	chr13:38221800-38239400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:38222800-38224400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:38223200-38225000	Weak transcription	NHDF-Ad	bronchial
15	chr13:38223400-38226600	Weak transcription	Hela-S3	cervix
16	chr13:38223600-38225000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:38223600-38225600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:38223600-38225600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr13:38223600-38229200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:38223800-38225800	Strong transcription	Osteobl	bone
21	chr13:38224000-38225600	Strong transcription	H1 Cell Line	embryonic stem cell

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