Variant report

Variant	rs2586416
Chromosome Location	chr1:172270226-172270227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10158839	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs10489287	0.84[CEU][hapmap]
rs10797969	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs11590165	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12038494	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12041600	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12737669	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12740971	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1992550	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1992551	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2224567	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs2255690	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2757504	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41481754	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs4916245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs508742	0.88[ASW][hapmap]
rs520918	0.81[AMR][1000 genomes]
rs6424841	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424865	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694387	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9425283	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9425287	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs9425560	0.84[CEU][hapmap];0.88[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006542	chr1:172253765-172304690	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2586416	FMO1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172256200-172290000	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:172256400-172290200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:172256600-172289800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:172260600-172271000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:172267600-172271000	Weak transcription	Left Ventricle	heart
6	chr1:172267800-172271400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:172267800-172272800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:172269000-172273200	Weak transcription	Brain Angular Gyrus	brain

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