Variant report

Variant	rs1458060
Chromosome Location	chr3:56046642-56046643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12631548	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1458061	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17056288	0.85[EUR][1000 genomes]
rs17216524	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17825124	0.95[EUR][1000 genomes]
rs4974160	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57141558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6779691	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797314	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805331	0.82[EUR][1000 genomes]
rs73086924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73089182	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1012098	chr3:56040905-56055908	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1458060	ARHGEF3	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56033000-56052000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:56033200-56046800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:56039800-56052400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:56041600-56054400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:56041800-56054000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:56045600-56048600	Enhancers	Fetal Heart	heart
7	chr3:56046200-56047200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:56046200-56047200	Enhancers	Gastric	stomach
9	chr3:56046400-56047600	Enhancers	Stomach Mucosa	stomach
10	chr3:56046600-56047200	Enhancers	Fetal Brain Female	brain
11	chr3:56046600-56047400	Weak transcription	Fetal Intestine Large	intestine
12	chr3:56046600-56047600	Enhancers	Fetal Kidney	kidney

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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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