Variant report

Variant	rs2831004
Chromosome Location	chr21:28936984-28936985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1379664	0.81[EUR][1000 genomes]
rs1457923	0.90[AFR][1000 genomes]
rs1457924	0.80[EUR][1000 genomes]
rs1457925	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2219408	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9305318	0.81[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	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv459229	chr21:28543456-29482488	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv587342	chr21:28543456-29482488	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv834071	chr21:28806911-28988880	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv587346	chr21:28921690-28942922	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv587347	chr21:28930833-28951567	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv913669	chr21:28932087-28981553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2831004	GRIK1	cis	cerebellum	SCAN
rs2831004	NLRC5	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28928400-28937600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:28929800-28937400	Weak transcription	NHLF	lung
3	chr21:28934000-28937200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:28934000-28937200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr21:28934000-28937200	Weak transcription	Fetal Lung	lung
6	chr21:28934000-28937800	Weak transcription	NHEK	skin
7	chr21:28934000-28941800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr21:28934200-28938800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr21:28934600-28941200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr21:28936200-28938000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:28936600-28939200	Enhancers	Osteobl	bone

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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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