Variant report

Variant	rs12639506
Chromosome Location	chr3:89480265-89480266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1028013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054750	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1157607	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1157608	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12152372	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12629165	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12629758	0.86[AMR][1000 genomes]
rs12631313	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12633325	0.83[AMR][1000 genomes]
rs12634269	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12634341	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12636710	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1499780	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1512183	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1512185	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17026944	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17026990	0.81[AMR][1000 genomes]
rs17801001	1.00[JPT][hapmap]
rs17801031	1.00[JPT][hapmap]
rs17801380	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1912965	0.95[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1912966	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2048518	0.81[AMR][1000 genomes]
rs2048519	0.84[AMR][1000 genomes]
rs2048520	0.81[AMR][1000 genomes]
rs2048521	0.81[AMR][1000 genomes]
rs2117138	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2346836	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2346840	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2881488	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3762717	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59541469	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60759140	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6551412	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66708608	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782527	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6795074	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6800436	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73137381	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73137382	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73137384	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73137387	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73137393	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73137395	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73139104	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73139105	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139110	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139115	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139117	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139118	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139119	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73139121	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73139125	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73139127	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73139129	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73139131	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73139133	0.80[EUR][1000 genomes]
rs73139134	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73139135	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73139139	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73139144	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73139147	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73139148	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73139257	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139261	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139276	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139281	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73139284	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73139286	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73139288	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73139290	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73139296	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73139302	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73141104	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73141108	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73141113	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73144998	0.81[AMR][1000 genomes]
rs73146907	0.86[AMR][1000 genomes]
rs73146968	0.86[AMR][1000 genomes]
rs73146970	0.86[AMR][1000 genomes]
rs73146972	0.81[AMR][1000 genomes]
rs73149113	0.86[AMR][1000 genomes]
rs73149115	0.81[AMR][1000 genomes]
rs7615949	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs7616322	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7650466	0.95[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs870898	1.00[JPT][hapmap]
rs870899	1.00[JPT][hapmap]
rs972030	0.86[AMR][1000 genomes]
rs9842599	0.81[MEX][hapmap]
rs9844971	1.00[JPT][hapmap]
rs9854073	1.00[JPT][hapmap]

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	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3331081	chr3:89479262-89483260	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12639506	EPHA3	cis	Frontal Cortex	GTEx
rs12639506	EPHA3	cis	Temporal Cortex	GTEx
rs12639506	EPHA3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89460800-89521200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:89469400-89483400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:89478400-89482400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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