Variant report

Variant	rs1512185
Chromosome Location	chr3:89473615-89473616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1028013	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1054750	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1157607	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs1157608	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12152372	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12629165	0.84[EUR][1000 genomes]
rs12631313	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12634269	0.84[EUR][1000 genomes]
rs12634341	0.83[EUR][1000 genomes]
rs12636710	0.95[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs12639506	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]
rs1499780	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1512183	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17026938	0.82[YRI][hapmap]
rs17026944	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs17801001	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17801031	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17801380	0.92[EUR][1000 genomes]
rs1912965	0.95[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs1912966	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2117138	0.84[EUR][1000 genomes]
rs2346836	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2346840	0.83[EUR][1000 genomes]
rs28623022	0.80[ASN][1000 genomes]
rs2881488	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3762717	0.95[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs57670516	0.80[ASN][1000 genomes]
rs59541469	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60759140	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62275018	0.80[ASN][1000 genomes]
rs62275019	0.80[ASN][1000 genomes]
rs6551412	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66708608	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6782527	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6795074	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs6800041	0.80[ASN][1000 genomes]
rs6800436	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs73137381	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137382	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73137387	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137393	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137395	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73139104	0.90[EUR][1000 genomes]
rs73139105	0.93[EUR][1000 genomes]
rs73139110	0.93[EUR][1000 genomes]
rs73139115	0.93[EUR][1000 genomes]
rs73139117	0.93[EUR][1000 genomes]
rs73139118	0.93[EUR][1000 genomes]
rs73139119	0.91[EUR][1000 genomes]
rs73139121	0.92[EUR][1000 genomes]
rs73139125	0.93[EUR][1000 genomes]
rs73139127	0.92[EUR][1000 genomes]
rs73139129	0.92[EUR][1000 genomes]
rs73139131	0.91[EUR][1000 genomes]
rs73139134	0.80[EUR][1000 genomes]
rs73139135	0.85[EUR][1000 genomes]
rs73139139	0.85[EUR][1000 genomes]
rs73139144	0.85[EUR][1000 genomes]
rs73139147	0.85[EUR][1000 genomes]
rs73139148	0.85[EUR][1000 genomes]
rs73139257	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73139261	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73139276	0.94[EUR][1000 genomes]
rs73139281	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139284	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139286	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139288	0.95[EUR][1000 genomes]
rs73139290	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139296	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73139302	0.94[EUR][1000 genomes]
rs73141104	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73141108	0.93[EUR][1000 genomes]
rs73141113	0.93[EUR][1000 genomes]
rs7615949	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7616322	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7626735	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs7631682	0.85[CHB][hapmap]
rs7645408	0.82[ASN][1000 genomes]
rs7650466	0.95[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs870898	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs870899	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9832305	0.85[CHB][hapmap]
rs9836340	0.85[CHB][hapmap]
rs9842599	0.85[CHB][hapmap]
rs9844971	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9849029	0.80[ASN][1000 genomes]
rs9854073	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9864984	0.80[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1512185	EPHA3	cis	Frontal Cortex	GTEx
rs1512185	EPHA3	cis	Temporal Cortex	GTEx
rs1512185	EPHA3	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89460800-89521200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:89463800-89478600	Weak transcription	Fetal Brain Female	brain
3	chr3:89469400-89483400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:89472600-89478400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:89473600-89474000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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