Variant report

Variant	rs1548136
Chromosome Location	chr3:22457403-22457404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11129055	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11129060	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap]
rs11129061	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12492984	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs13061996	0.84[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs1494228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs1494230	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap]
rs2047156	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs2047159	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2198020	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap]
rs3749375	0.92[MEX][hapmap];0.80[AMR][1000 genomes]
rs4431131	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs4858035	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs6768103	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6778816	0.86[YRI][hapmap]
rs6789629	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs7610597	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs7642830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7645719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs935737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs9798951	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs982354	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs986483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs9882784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003211	chr3:22244883-22584229	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv536520	chr3:22244883-22584229	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv428082	chr3:22397625-22539817	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv834634	chr3:22420053-22574021	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1548136	NGLY1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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