Variant report

Variant	rs71456716
Chromosome Location	chr12:122310347-122310348
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10840625	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12817002	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2707061	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3741591	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825172	0.94[AFR][1000 genomes]
rs55826938	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56177852	0.94[AFR][1000 genomes]
rs58379261	0.94[AFR][1000 genomes]
rs59517025	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs71456717	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302187	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7309105	0.94[AFR][1000 genomes]
rs7969647	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs71456716	HPD	cis	Muscle Skeletal	GTEx
rs71456716	RP11-7M8.2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122300200-122310800	Weak transcription	Placenta	Placenta
2	chr12:122301600-122312800	Weak transcription	Liver	Liver
3	chr12:122301600-122312800	Weak transcription	HepG2	liver
4	chr12:122304800-122310800	Weak transcription	NHDF-Ad	bronchial
5	chr12:122305400-122310600	Weak transcription	Fetal Brain Male	brain
6	chr12:122306200-122311000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:122306600-122310800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:122308800-122311000	Enhancers	K562	blood
9	chr12:122309400-122312200	Enhancers	Fetal Stomach	stomach
10	chr12:122309600-122310400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:122310200-122310400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:122310200-122310400	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr12:122310200-122311000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:122310200-122311200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:122310200-122311400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:122310200-122311400	Enhancers	NHLF	lung
17	chr12:122310200-122311400	Enhancers	Osteobl	bone

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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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