Variant report

Variant	rs13398112
Chromosome Location	chr2:67828614-67828615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10172154	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10174552	0.80[AFR][1000 genomes]
rs10191798	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17033861	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28838983	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2902021	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2902026	0.94[JPT][hapmap]
rs6546324	0.94[JPT][hapmap]
rs7423926	0.80[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13398112	NAGK	cis	parietal	SCAN
rs13398112	ADD2	cis	cerebellum	SCAN
rs13398112	ETAA1	cis	cerebellum	SCAN
rs13398112	FAM136A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67813600-67828800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:67826200-67829000	Enhancers	HMEC	breast
3	chr2:67826400-67829000	Enhancers	NHDF-Ad	bronchial
4	chr2:67827000-67831000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:67827200-67831000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:67828000-67839400	Weak transcription	Placenta	Placenta
7	chr2:67828400-67831000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:67828400-67831200	Weak transcription	HSMMtube	muscle
9	chr2:67828600-67830200	Weak transcription	NHLF	lung

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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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