Variant report

Variant	rs7546899
Chromosome Location	chr1:56076299-56076300
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10493196	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10749702	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11206625	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11206629	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11206636	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206637	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206638	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11206639	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807964	0.96[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12026971	0.96[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12040862	0.96[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12041985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12086546	0.83[EUR][1000 genomes]
rs12132336	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139752	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142554	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12401977	0.83[EUR][1000 genomes]
rs1392128	0.96[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1392129	0.96[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1392130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1392131	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1392132	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1587432	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1604016	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17112402	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17417716	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17452876	0.84[CEU][hapmap]
rs56169646	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61776360	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61776375	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61776377	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6669248	0.85[EUR][1000 genomes]
rs6675850	0.82[AMR][1000 genomes]
rs709397	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7513395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525515	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7544458	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556008	0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs769971	0.89[ASN][1000 genomes]
rs769984	0.89[ASN][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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:56071600-56076400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:56074200-56076600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:56074400-56077200	Weak transcription	Placenta	Placenta
5	chr1:56075400-56077400	Enhancers	Osteobl	bone
6	chr1:56075400-56080000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:56075600-56076400	Enhancers	HepG2	liver
8	chr1:56075800-56079200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:56076000-56076600	Enhancers	Aorta	Aorta
10	chr1:56076000-56076800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:56076000-56077200	Enhancers	Fetal Lung	lung
12	chr1:56076000-56077400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:56076000-56077600	Enhancers	Ovary	ovary
14	chr1:56076000-56079400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:56076200-56076800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:56076200-56077400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:56076200-56079200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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