Variant report

Variant	rs28397978
Chromosome Location	chr2:142279803-142279804
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11902750	1.00[AMR][1000 genomes]
rs16846255	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846284	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846309	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73963309	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73963311	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73963312	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73963379	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7569388	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7595586	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv470491	chr2:142254119-142299923	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv834393	chr2:142256714-142431564	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	nsv583210	chr2:142259592-142295042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv459629	chr2:142263400-142295042	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv583211	chr2:142263400-142295042	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv583212	chr2:142263979-142309330	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142278200-142280600	Enhancers	Brain Substantia Nigra	brain
2	chr2:142278600-142280000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:142278800-142291200	Weak transcription	Brain Anterior Caudate	brain
4	chr2:142279000-142280000	Weak transcription	Brain Angular Gyrus	brain
5	chr2:142279400-142280000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr2:142279600-142280000	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:142279600-142280200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:142279600-142280600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:142279600-142280600	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:142279800-142280800	Bivalent Enhancer	Fetal Heart	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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