Variant report

Variant	rs12890679
Chromosome Location	chr14:65662491-65662492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1123493	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12897052	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17102477	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17826026	0.81[ASN][1000 genomes]
rs55839896	0.81[ASN][1000 genomes]
rs56116751	1.00[ASN][1000 genomes]
rs8017695	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832817	chr14:65637069-65810406	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv564932	chr14:65660502-65691545	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12890679	GLT25D1	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65660600-65663000	Enhancers	Primary B cells from peripheral blood	blood
2	chr14:65661000-65662600	Enhancers	HepG2	liver
3	chr14:65661400-65665000	Weak transcription	Fetal Intestine Large	intestine
4	chr14:65661400-65665000	Weak transcription	Fetal Intestine Small	intestine
5	chr14:65661600-65663000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr14:65661800-65663000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr14:65661800-65663000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr14:65662200-65662800	Flanking Active TSS	GM12878-XiMat	blood
9	chr14:65662400-65662600	Enhancers	Brain Substantia Nigra	brain

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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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