Variant report

Variant	rs11921985
Chromosome Location	chr3:89467357-89467358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12636275	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2117137	0.96[CEU][hapmap];0.95[MEX][hapmap];0.86[EUR][1000 genomes]
rs35124509	0.96[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35968370	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792572	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67316928	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6771054	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6772953	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7632502	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637670	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7650184	0.88[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs987748	0.96[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11921985	EPHA3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89458600-89468000	Weak transcription	Left Ventricle	heart
2	chr3:89460800-89521200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:89463800-89478600	Weak transcription	Fetal Brain Female	brain
4	chr3:89465200-89471800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:89466800-89467800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:89467200-89468800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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