Variant report

Variant	rs2892180
Chromosome Location	chr20:24400058-24400059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1997790	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2103702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223648	0.94[MKK][hapmap]
rs4813522	1.00[ASW][hapmap]
rs6036762	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6036766	0.87[EUR][1000 genomes]
rs6036770	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049644	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049656	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049660	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106872	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106873	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv833946	chr20:24320375-24490702	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2892180	INSM1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24399400-24400200	Enhancers	Brain Anterior Caudate	brain
2	chr20:24399600-24400400	Enhancers	Brain Hippocampus Middle	brain
3	chr20:24399600-24401600	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr20:24399800-24400200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:24399800-24400200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr20:24399800-24400200	Enhancers	NH-A	brain
7	chr20:24400000-24400200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr20:24400000-24400200	Enhancers	Aorta	Aorta
9	chr20:24400000-24400600	Enhancers	Brain Cingulate Gyrus	brain
10	chr20:24400000-24400800	Weak transcription	Brain Substantia Nigra	brain
11	chr20:24400000-24401400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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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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