Variant report

Variant	rs4385792
Chromosome Location	chr10:28284404-28284405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10826379	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006790	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006798	0.82[CHB][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11595811	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12218330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1419365	0.82[CEU][hapmap]
rs4747609	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4747610	0.83[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs4747611	0.82[CHB][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4749292	0.85[EUR][1000 genomes]
rs4749293	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs6481497	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7076786	0.82[AMR][1000 genomes]
rs7095042	0.81[EUR][1000 genomes]
rs7917840	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9416763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv894987	chr10:28165502-28326775	ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831815	chr10:28235661-28407533	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1052182	chr10:28259142-28361830	Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4385792	MYO3A	cis	cerebellum	SCAN
rs4385792	PDSS1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28239800-28287200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:28283800-28285000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr10:28283800-28286000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:28283800-28286600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:28283800-28286600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr10:28284000-28284600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:28284000-28285000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:28284000-28285400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr10:28284200-28285400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:28284400-28284600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr10:28284400-28284800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr10:28284400-28286800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:28284400-28286800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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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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