Variant report

Variant	rs12134777
Chromosome Location	chr1:171138681-171138682
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10798240	0.84[AMR][1000 genomes]
rs10798253	0.81[AMR][1000 genomes]
rs10912475	0.84[AMR][1000 genomes]
rs10912478	1.00[ASN][1000 genomes]
rs10912484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912486	0.83[ASN][1000 genomes]
rs10912503	0.83[ASN][1000 genomes]
rs10912504	0.83[ASN][1000 genomes]
rs10912524	0.82[ASN][1000 genomes]
rs11803918	0.83[ASN][1000 genomes]
rs11804100	0.83[ASN][1000 genomes]
rs11806072	0.88[CEU][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs11806352	0.83[ASN][1000 genomes]
rs11806405	0.83[ASN][1000 genomes]
rs11807206	0.83[ASN][1000 genomes]
rs12129672	1.00[ASN][1000 genomes]
rs12132443	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133379	0.83[ASN][1000 genomes]
rs12136568	1.00[ASN][1000 genomes]
rs12406402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408043	0.83[ASN][1000 genomes]
rs12408253	0.82[ASN][1000 genomes]
rs12566068	0.82[ASN][1000 genomes]
rs12729618	0.98[ASN][1000 genomes]
rs12744605	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008706	0.82[AMR][1000 genomes]
rs2075987	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs2075990	0.87[MEX][hapmap]
rs2179105	0.87[MEX][hapmap]
rs2205730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205732	0.83[ASN][1000 genomes]
rs2236874	0.88[CEU][hapmap]
rs2421707	0.98[ASN][1000 genomes]
rs2421709	0.81[AMR][1000 genomes]
rs2901513	0.98[ASN][1000 genomes]
rs3754494	0.81[AMR][1000 genomes]
rs3768570	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs4916410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61814303	1.00[ASN][1000 genomes]
rs6608456	0.98[ASN][1000 genomes]
rs6657314	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs7531111	0.81[ASN][1000 genomes]
rs7887295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7891433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926268	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs9730437	0.83[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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12134777	FMO3	cis	cerebellum	SCAN
rs12134777	FMO2	cis	parietal	SCAN
rs12134777	FMO2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171136400-171139000	Weak transcription	Fetal Lung	lung
2	chr1:171137800-171142200	Weak transcription	Stomach Mucosa	stomach
3	chr1:171138400-171139200	Enhancers	Esophagus	oesophagus

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