Variant report

Variant	rs2219408
Chromosome Location	chr21:28954645-28954646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13049964	0.87[ASN][1000 genomes]
rs1379664	0.84[EUR][1000 genomes]
rs1457923	0.80[EUR][1000 genomes]
rs1457924	0.84[EUR][1000 genomes]
rs1457925	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2831004	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9305318	0.84[EUR][1000 genomes]
rs9305320	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2219408	GRIK1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28952000-28955200	Enhancers	NHEK	skin
2	chr21:28952000-28957200	Enhancers	Osteobl	bone
3	chr21:28952400-28962200	Weak transcription	HSMM	muscle
4	chr21:28953600-28957200	Enhancers	NHDF-Ad	bronchial
5	chr21:28953600-28957600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr21:28953800-28955200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr21:28953800-28957200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr21:28954200-28955400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr21:28954200-28955400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr21:28954200-28955400	Enhancers	HMEC	breast
11	chr21:28954400-28954800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr21:28954400-28955000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:28954400-28955400	Enhancers	NHLF	lung
14	chr21:28954600-28955000	Enhancers	NH-A	brain
15	chr21:28954600-28956000	Enhancers	Muscle Satellite Cultured Cells	--

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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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