Variant report

Variant	rs1496519
Chromosome Location	chr3:89046168-89046169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13067189	1.00[AFR][1000 genomes]
rs1390697	1.00[AFR][1000 genomes]
rs1390707	1.00[AFR][1000 genomes]
rs1496511	1.00[AFR][1000 genomes]
rs1496516	1.00[AFR][1000 genomes]
rs1496517	1.00[AFR][1000 genomes]
rs1496520	1.00[AFR][1000 genomes]
rs1603448	1.00[AFR][1000 genomes]
rs2088302	1.00[AFR][1000 genomes]
rs2132586	1.00[AFR][1000 genomes]
rs2173041	1.00[AFR][1000 genomes]
rs2173042	1.00[AFR][1000 genomes]
rs2881280	1.00[AFR][1000 genomes]
rs4364170	1.00[AFR][1000 genomes]
rs4452333	1.00[AFR][1000 genomes]
rs4855795	1.00[AFR][1000 genomes]
rs4855824	1.00[AFR][1000 genomes]
rs6788395	1.00[AFR][1000 genomes]
rs6792141	1.00[AFR][1000 genomes]
rs7613904	1.00[AFR][1000 genomes]
rs903893	1.00[AFR][1000 genomes]
rs9284816	1.00[AFR][1000 genomes]
rs9844121	1.00[AFR][1000 genomes]
rs9876056	1.00[YRI][hapmap]
rs9880925	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834759	chr3:88901229-89105366	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1002060	chr3:88984502-89047104	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv536637	chr3:88984502-89047104	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv877158	chr3:89018866-89103302	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv525314	chr3:89031440-89051475	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	n/a	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	chr3:89045000-89046800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:89045000-89047200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:89045600-89046400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:89045600-89046400	Enhancers	Brain Anterior Caudate	brain
5	chr3:89045600-89046400	Enhancers	Colon Smooth Muscle	Colon
6	chr3:89045600-89046800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:89045600-89047400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:89045800-89046200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:89045800-89046400	Bivalent Enhancer	HSMMtube	muscle
10	chr3:89045800-89046600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:89045800-89046800	Enhancers	Brain Hippocampus Middle	brain
12	chr3:89045800-89046800	Enhancers	Fetal Heart	heart
13	chr3:89045800-89047000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:89045800-89047200	Enhancers	HMEC	breast
15	chr3:89045800-89047200	Enhancers	NHEK	skin
16	chr3:89046000-89046200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr3:89046000-89046400	Enhancers	Brain Substantia Nigra	brain
18	chr3:89046000-89047000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:89046000-89047200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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