Variant report

Variant	rs6694025
Chromosome Location	chr1:239862101-239862102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10925968	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10925969	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1135	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12059584	1.00[ASN][1000 genomes]
rs12062155	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062192	1.00[ASN][1000 genomes]
rs12354162	1.00[ASN][1000 genomes]
rs13376649	1.00[ASN][1000 genomes]
rs16832149	1.00[ASN][1000 genomes]
rs16838584	1.00[ASN][1000 genomes]
rs16838623	1.00[ASN][1000 genomes]
rs16838631	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838669	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838681	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838689	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838720	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838848	1.00[ASN][1000 genomes]
rs16838871	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838874	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838878	1.00[ASN][1000 genomes]
rs28448804	0.81[EUR][1000 genomes]
rs4145784	1.00[ASN][1000 genomes]
rs61834772	1.00[ASN][1000 genomes]
rs61834776	1.00[ASN][1000 genomes]
rs61834781	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834783	1.00[ASN][1000 genomes]
rs61834785	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834786	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834816	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834817	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834821	0.81[AMR][1000 genomes]
rs61834822	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834823	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834825	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834826	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834828	1.00[ASN][1000 genomes]
rs61834842	1.00[ASN][1000 genomes]
rs61834844	1.00[ASN][1000 genomes]
rs61834845	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834846	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834847	1.00[ASN][1000 genomes]
rs61836595	1.00[ASN][1000 genomes]
rs6661636	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516378	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7523711	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527723	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6694025	OPN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239845000-239879800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:239858400-239868200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:239859800-239869600	Weak transcription	Pancreas	Pancrea
4	chr1:239860000-239863800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:239861200-239878000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:239861400-239867200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:239861400-239871600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:239862000-239864400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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