Variant report

Variant	rs12038695
Chromosome Location	chr1:215377957-215377958
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10864166	0.88[CEU][hapmap]
rs11120504	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs11120519	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs11120581	0.88[CEU][hapmap]
rs11583745	0.85[CEU][hapmap]
rs12038616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12740245	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs12753507	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs1538547	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17024500	0.88[CEU][hapmap];0.81[CHD][hapmap]
rs2027320	0.81[TSI][hapmap]
rs2363563	0.91[CHB][hapmap]
rs4233309	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5025775	0.88[CEU][hapmap]
rs6540886	0.88[CEU][hapmap];0.81[CHD][hapmap]
rs6540887	0.88[CEU][hapmap]
rs6670661	0.88[CEU][hapmap]
rs7522552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528475	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
2	nsv873170	chr1:215367248-215440975	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	esv2760086	chr1:215370570-215381265	Enhancers Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12038695	USH2A	cis	cerebellum	SCAN
rs12038695	G0S2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215374800-215380000	Weak transcription	Osteobl	bone
2	chr1:215375000-215379600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:215375000-215387200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:215376400-215378200	Weak transcription	NHDF-Ad	bronchial

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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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