Variant report

Variant	rs10925969
Chromosome Location	chr1:239913038-239913039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1030591	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10925968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1135	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059584	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062192	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066872	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12093210	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12354162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376649	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832149	1.00[ASN][1000 genomes]
rs16838584	1.00[ASN][1000 genomes]
rs16838623	1.00[ASN][1000 genomes]
rs16838631	1.00[ASN][1000 genomes]
rs16838669	1.00[ASN][1000 genomes]
rs16838681	1.00[ASN][1000 genomes]
rs16838689	1.00[ASN][1000 genomes]
rs16838720	1.00[ASN][1000 genomes]
rs16838848	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838874	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145784	1.00[ASN][1000 genomes]
rs61834772	1.00[ASN][1000 genomes]
rs61834776	1.00[ASN][1000 genomes]
rs61834781	1.00[ASN][1000 genomes]
rs61834783	1.00[ASN][1000 genomes]
rs61834785	1.00[ASN][1000 genomes]
rs61834786	1.00[ASN][1000 genomes]
rs61834816	1.00[ASN][1000 genomes]
rs61834817	1.00[ASN][1000 genomes]
rs61834822	1.00[ASN][1000 genomes]
rs61834823	1.00[ASN][1000 genomes]
rs61834825	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61834826	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61834828	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834837	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61834838	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61834839	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61834840	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61834842	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834844	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61836595	1.00[ASN][1000 genomes]
rs61836669	0.81[EUR][1000 genomes]
rs6661636	1.00[ASN][1000 genomes]
rs6694025	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516378	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523711	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527723	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv35011	chr1:239907420-240298959	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv2756891	chr1:239907420-240308147	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv873353	chr1:239913038-240253320	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv873354	chr1:239913038-240303322	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10925969	OPN3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239889000-239949800	Weak transcription	Pancreas	Pancrea
2	chr1:239891200-239918400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:239906000-239923000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:239906200-239915800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:239908600-239915000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:239908800-239916600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:239910000-239913200	Weak transcription	Fetal Stomach	stomach
8	chr1:239912400-239916000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links