Variant report

Variant	rs9815025
Chromosome Location	chr3:89215213-89215214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:89207136..89210104-chr3:89214868..89216855,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11128071	0.85[YRI][hapmap]
rs12629427	0.87[ASN][1000 genomes]
rs12637863	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13315867	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13326166	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4425279	0.84[ASW][hapmap];0.82[CHB][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs59012690	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6551393	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6551394	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6551396	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6551400	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551401	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768846	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802483	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72919895	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72921746	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374085	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433757	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611735	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7612982	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630371	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631328	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639401	0.94[YRI][hapmap]
rs7641811	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7647240	0.84[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs9310117	0.94[LWK][hapmap];0.80[YRI][hapmap]
rs9809011	0.80[YRI][hapmap]
rs9810366	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9821502	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832319	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834174	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834433	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9838527	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842523	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843199	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9848187	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9854754	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9860797	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9868838	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878894	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883005	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9883387	0.84[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9883681	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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
2	nsv1005603	chr3:89174152-89223459	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv997874	chr3:89188275-89279573	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1008916	chr3:89206065-89241915	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9815025	EPHA3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89211600-89217400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr3:89213400-89218400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:89213600-89216200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:89213800-89216200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:89214000-89215600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:89214000-89215800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:89214000-89217400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:89214000-89218200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:89214400-89215400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:89214800-89215600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:89215000-89215400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:89215000-89215400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr3:89215000-89215400	Enhancers	Brain Germinal Matrix	brain
14	chr3:89215000-89217400	Weak transcription	Brain Anterior Caudate	brain
15	chr3:89215200-89215400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:89215200-89217200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:89215200-89221000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:89215200-89221000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:89215200-89221400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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