Variant report

Variant	rs12629427
Chromosome Location	chr3:89145340-89145341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11128071	0.80[YRI][hapmap]
rs12637863	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13315867	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13326166	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4425279	0.84[ASW][hapmap];0.82[CHB][hapmap];0.84[YRI][hapmap]
rs6551393	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6551394	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6551396	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6551400	0.87[ASN][1000 genomes]
rs6551401	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs6768846	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6802483	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs72919895	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72921746	0.87[ASN][1000 genomes]
rs7374085	0.87[ASN][1000 genomes]
rs7433757	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs7611735	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7612982	0.87[ASN][1000 genomes]
rs7630371	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7631328	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7639401	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs7641811	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7647240	0.84[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs9310117	0.88[LWK][hapmap]
rs9810366	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9815025	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs9821502	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9832319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9834174	0.87[ASN][1000 genomes]
rs9834433	0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs9838527	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9842523	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9843199	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9848187	0.85[EUR][1000 genomes]
rs9854754	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9860797	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868838	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878894	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9883005	0.85[ASN][1000 genomes]
rs9883387	0.85[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9883681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[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	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12629427	EPHA3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89145200-89145800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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