Variant report

Variant	rs2879547
Chromosome Location	chr10:52860117-52860118
allele	C/T
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:19)

rs_ID	r²[population]
rs10822178	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs10822190	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12355844	0.89[EUR][1000 genomes]
rs2339628	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2339673	0.89[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2339678	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2879523	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4603249	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4935010	0.84[EUR][1000 genomes]
rs4935011	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4935216	0.81[EUR][1000 genomes]
rs4935221	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4935228	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7904024	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9414823	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9415718	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9415721	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9415730	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs987633	0.81[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	nsv831873	chr10:52710610-52899540	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv895394	chr10:52793177-52866503	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1036645	chr10:52804961-53159076	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv825378	chr10:52855771-52908439	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52844000-52877200	Weak transcription	Fetal Stomach	stomach
2	chr10:52850200-52863400	Weak transcription	NHLF	lung
3	chr10:52853000-52871200	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:52855200-52866200	Weak transcription	Psoas Muscle	Psoas
5	chr10:52856400-52861800	Weak transcription	Right Atrium	heart
6	chr10:52856600-52877200	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:52857600-52877200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:52858200-52860200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:52858800-52866200	Weak transcription	Left Ventricle	heart
10	chr10:52858800-52873000	Weak transcription	Aorta	Aorta
11	chr10:52859400-52863400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:52859600-52863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:52859800-52860600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:52860000-52866000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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