Variant report

Variant	rs690394
Chromosome Location	chr15:53403576-53403577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12442118	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs528534	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs559546	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs580689	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs585020	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs608531	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs615229	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493610	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs689681	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs690176	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs690275	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833007	chr15:53264564-53453525	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv904221	chr15:53279378-53434365	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3343986	chr15:53284440-53571936	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1037630	chr15:53324645-53708925	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1050535	chr15:53352572-53472957	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1039762	chr15:53354285-53414479	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs690394	TRPM7	cis	cerebellum	SCAN
rs690394	MAPK6	cis	cerebellum	SCAN
rs690394	FBN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53402400-53404400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr15:53402600-53404000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr15:53402600-53404000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr15:53402600-53404400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr15:53402600-53404800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:53402800-53403600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:53402800-53403600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr15:53403000-53404200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr15:53403000-53404400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr15:53403400-53403600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:53403400-53403800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr15:53403400-53403800	Enhancers	H9 Cell Line	embryonic stem cell
13	chr15:53403400-53403800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

Quick Search:

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

what's new

Quick links