Variant report

Variant	rs11720002
Chromosome Location	chr3:53709642-53709643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11130377	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11711045	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711142	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715072	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11925053	0.82[EUR][1000 genomes]
rs1460118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17238364	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs1870564	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2250736	1.00[CHB][hapmap]
rs2680656	0.89[CHB][hapmap]
rs58086880	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60529666	0.85[EUR][1000 genomes]
rs6780648	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6786135	0.94[CHB][hapmap]
rs6804675	0.87[YRI][hapmap]
rs6809164	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs898411	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs898418	0.89[ASN][1000 genomes]

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	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53698000-53714000	Weak transcription	Brain Substantia Nigra	brain
3	chr3:53698800-53711200	Weak transcription	Spleen	Spleen
4	chr3:53700600-53709800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:53705000-53710000	Enhancers	Fetal Lung	lung
6	chr3:53705400-53710600	Strong transcription	Fetal Intestine Small	intestine
7	chr3:53706200-53710800	Strong transcription	Fetal Intestine Large	intestine
8	chr3:53708200-53713600	Weak transcription	Fetal Brain Female	brain
9	chr3:53708400-53710000	Enhancers	Fetal Heart	heart
10	chr3:53708400-53711800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:53708600-53710200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr3:53708600-53710600	Weak transcription	Fetal Kidney	kidney
13	chr3:53708800-53711200	Weak transcription	Lung	lung
14	chr3:53708800-53711200	Weak transcription	Right Atrium	heart
15	chr3:53709000-53714000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:53709400-53710000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:53709400-53713800	Weak transcription	Fetal Brain Male	brain

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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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