Variant report

Variant	rs2456020
Chromosome Location	chr15:78868398-78868399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11637630	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12910984	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13329271	0.83[EUR][1000 genomes]
rs1700006	0.84[EUR][1000 genomes]
rs1711731	0.84[EUR][1000 genomes]
rs3743078	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825845	0.89[EUR][1000 genomes]
rs4887069	0.87[EUR][1000 genomes]
rs518425	0.85[AMR][1000 genomes]
rs564585	0.81[AMR][1000 genomes]
rs569207	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs576982	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs578776	0.85[AMR][1000 genomes]
rs637137	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6495308	0.90[EUR][1000 genomes]
rs6495309	0.84[EUR][1000 genomes]
rs664172	0.83[EUR][1000 genomes]
rs667282	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7177514	0.90[EUR][1000 genomes]
rs7183604	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7359276	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8042059	0.90[EUR][1000 genomes]
rs8042374	0.90[EUR][1000 genomes]
rs8042494	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8043009	0.90[EUR][1000 genomes]
rs938682	0.86[AMR][1000 genomes];0.90[EUR][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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
3	esv1818155	chr15:78866785-78874073	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2456020	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2456020	CHRNA5	cis	Muscle Skeletal	GTEx
rs2456020	CHRNA3	cis	Muscle Skeletal	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78859000-78868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78859200-78882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:78860200-78881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:78860200-78881600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:78860200-78882200	Weak transcription	Hela-S3	cervix
6	chr15:78864600-78869200	Weak transcription	A549	lung
7	chr15:78865800-78873200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood

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Input of quick search could be:

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

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