Variant report

Variant	rs11120519
Chromosome Location	chr1:215387063-215387064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10779649	0.85[CHD][hapmap]
rs10779651	0.85[CHD][hapmap]
rs10864165	0.86[EUR][1000 genomes]
rs10864166	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10864169	0.83[EUR][1000 genomes]
rs11120508	0.80[CHD][hapmap]
rs11120513	0.80[CHD][hapmap]
rs11120524	0.88[EUR][1000 genomes]
rs11120530	0.81[EUR][1000 genomes]
rs11120581	0.84[CEU][hapmap]
rs1112101	0.84[CHD][hapmap]
rs11583745	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs11588455	0.81[EUR][1000 genomes]
rs12026669	0.80[EUR][1000 genomes]
rs12026702	0.80[EUR][1000 genomes]
rs12036046	0.83[EUR][1000 genomes]
rs12038616	0.88[CEU][hapmap]
rs12038695	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs12044688	0.83[EUR][1000 genomes]
rs12047082	0.81[EUR][1000 genomes]
rs12049601	0.83[EUR][1000 genomes]
rs12567520	0.85[CHD][hapmap]
rs12740245	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs12750276	0.81[EUR][1000 genomes]
rs12752882	0.81[EUR][1000 genomes]
rs12753507	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs1416661	0.80[EUR][1000 genomes]
rs1538544	0.80[EUR][1000 genomes]
rs1538547	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs1556905	0.90[CHB][hapmap]
rs17024500	0.92[CEU][hapmap]
rs2027320	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs2153244	0.88[EUR][1000 genomes]
rs2363557	0.82[CHD][hapmap]
rs2363564	0.80[CHD][hapmap]
rs2363565	0.80[CHD][hapmap]
rs2363566	0.85[CHD][hapmap]
rs2363567	0.85[CHD][hapmap]
rs3933352	0.82[EUR][1000 genomes]
rs4098470	0.83[EUR][1000 genomes]
rs4098471	0.83[EUR][1000 genomes]
rs4233309	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4303048	0.85[CHD][hapmap]
rs4655394	0.83[CHD][hapmap]
rs4655397	0.82[EUR][1000 genomes]
rs4655398	0.82[EUR][1000 genomes]
rs4655399	0.83[EUR][1000 genomes]
rs4655400	0.80[EUR][1000 genomes]
rs5025775	0.92[CEU][hapmap]
rs6540886	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6540887	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs6662353	0.82[CHD][hapmap]
rs6670661	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6672978	0.80[CHD][hapmap]
rs6684084	0.85[CHD][hapmap]
rs7522160	0.82[EUR][1000 genomes]
rs7522552	0.88[CEU][hapmap]
rs7528475	0.80[CEU][hapmap]
rs946487	0.81[EUR][1000 genomes]
rs946488	0.83[EUR][1000 genomes]
rs946489	0.81[EUR][1000 genomes]
rs946490	0.82[EUR][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	esv3419500	chr1:215384229-215387127	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11120519	USH2A	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215375000-215387200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:215380600-215408000	Weak transcription	Osteobl	bone
3	chr1:215384800-215388800	Weak transcription	NHDF-Ad	bronchial
4	chr1:215384800-215391200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:215385400-215389600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:215386600-215388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:215386600-215388400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:215386600-215388800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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