Variant report

Variant	rs303539
Chromosome Location	chr10:90561586-90561587
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs303467	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303474	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303478	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303479	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303483	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303488	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303489	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303500	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs303502	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303531	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303532	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303537	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303541	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs367605	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3858283	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs399496	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs435742	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs814630	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs845134	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv831941	chr10:90410488-90587332	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1043015	chr10:90467067-90593692	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs303539	LIPN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90560800-90563600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr10:90560800-90563600	Weak transcription	Aorta	Aorta
3	chr10:90560800-90569600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:90561000-90562400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr10:90561000-90564400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr10:90561000-90564800	Weak transcription	Osteobl	bone
7	chr10:90561000-90565000	Weak transcription	NH-A	brain
8	chr10:90561200-90565000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

Quick Search:

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

what's new

Quick links