Variant report

Variant	rs6551407
Chromosome Location	chr3:89270605-89270606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11128071	0.93[JPT][hapmap]
rs11720651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13083092	0.80[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4132275	0.81[JPT][hapmap]
rs6419884	0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7373232	0.91[MEX][hapmap]
rs7432948	0.93[JPT][hapmap]
rs7609645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7612746	0.81[JPT][hapmap]
rs7633559	0.84[JPT][hapmap]
rs7646842	0.81[JPT][hapmap]
rs9852594	0.91[MEX][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	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	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
3	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
4	esv2757001	chr3:89260495-89271087	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv2759160	chr3:89260495-89271087	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6551407	EPHA3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89263600-89277000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:89266200-89272200	Weak transcription	Fetal Brain Male	brain
3	chr3:89266400-89277800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:89270200-89270800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:89270400-89271400	Enhancers	Fetal Brain Female	brain

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Input of quick search could be:

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

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