Variant report

Variant	rs10029654
Chromosome Location	chr4:110861927-110861928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10002971	0.85[EUR][1000 genomes]
rs10011112	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs10014383	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs10017261	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10023272	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10029105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10213531	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1024600	0.92[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10470911	0.96[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10488881	0.96[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11098056	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11568903	0.90[EUR][1000 genomes]
rs11568905	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11568950	0.96[EUR][1000 genomes]
rs11568972	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs11568994	0.83[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs17253063	0.86[EUR][1000 genomes]
rs2024114	0.96[EUR][1000 genomes]
rs2067004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2190909	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237041	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs2237045	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2250616	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2282785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298977	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2347136	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs28437404	0.95[EUR][1000 genomes]
rs28535066	0.94[EUR][1000 genomes]
rs28540029	0.98[EUR][1000 genomes]
rs28564978	0.98[EUR][1000 genomes]
rs28629923	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28672708	0.96[EUR][1000 genomes]
rs28734982	0.95[EUR][1000 genomes]
rs3764861	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3775967	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3796945	0.98[EUR][1000 genomes]
rs3796946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822288	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4279279	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4698755	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698756	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698800	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4698801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62327604	0.96[EUR][1000 genomes]
rs6533481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837717	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs7655579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668520	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680062	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs881878	0.96[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs9307347	0.95[EUR][1000 genomes]
rs9992755	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv1813951	chr4:110840748-110862637	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10029654	GAR1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110843000-110876200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:110852400-110873800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:110853800-110871200	Weak transcription	Left Ventricle	heart
4	chr4:110860600-110863200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:110860600-110906600	Weak transcription	Psoas Muscle	Psoas
6	chr4:110860800-110874800	Weak transcription	Pancreas	Pancrea

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