Variant report

Variant	rs59046245
Chromosome Location	chr9:98568552-98568553
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98562038..98564856-chr9:98568504..98570089,2	K562	blood:
2	chr9:98566028..98568952-chr9:98582785..98584307,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-3	chr9:98568370-98576204	NONHSAT133392
2	lnc-PTCH1-3	chr9:98568376-98570719	NONHSAT133393

Extended variants
information (count: 65 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12003772	0.88[ASN][1000 genomes]
rs12004258	0.90[AFR][1000 genomes]
rs12551596	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551880	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12554182	0.93[ASN][1000 genomes]
rs12555687	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413178	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910333	0.97[ASN][1000 genomes]
rs16910342	0.97[ASN][1000 genomes]
rs16910409	0.90[ASN][1000 genomes]
rs16910427	0.90[ASN][1000 genomes]
rs17303073	0.89[EUR][1000 genomes]
rs17303324	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297009	0.91[ASN][1000 genomes]
rs2423	0.90[ASN][1000 genomes]
rs3739755	0.95[ASN][1000 genomes]
rs3739756	0.88[ASN][1000 genomes]
rs3991704	0.90[AFR][1000 genomes]
rs4742763	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742801	0.91[ASN][1000 genomes]
rs4743327	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743351	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743383	0.97[ASN][1000 genomes]
rs4743460	0.88[ASN][1000 genomes]
rs4743469	0.81[ASN][1000 genomes]
rs55651016	0.97[ASN][1000 genomes]
rs55770584	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55781050	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797980	0.88[ASN][1000 genomes]
rs55870020	0.95[AFR][1000 genomes]
rs55881510	0.91[ASN][1000 genomes]
rs56063686	0.95[ASN][1000 genomes]
rs56070531	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56110216	0.91[ASN][1000 genomes]
rs56125887	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56275194	0.95[AFR][1000 genomes]
rs56372801	0.88[ASN][1000 genomes]
rs56403401	0.91[ASN][1000 genomes]
rs57096664	0.97[ASN][1000 genomes]
rs58715455	0.92[AFR][1000 genomes]
rs59189545	0.95[ASN][1000 genomes]
rs59510923	0.94[AFR][1000 genomes]
rs60301271	0.90[AFR][1000 genomes]
rs61036807	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61093440	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478983	0.94[AFR][1000 genomes]
rs7021641	0.95[AFR][1000 genomes]
rs7030427	0.95[AFR][1000 genomes]
rs7031397	0.94[AFR][1000 genomes]
rs7046189	0.95[AFR][1000 genomes]
rs7047126	0.92[AFR][1000 genomes]
rs73656542	0.97[AFR][1000 genomes]
rs73656543	0.97[AFR][1000 genomes]
rs73656554	0.94[AFR][1000 genomes]
rs73656561	0.95[AFR][1000 genomes]
rs73656564	0.95[AFR][1000 genomes]
rs7860019	0.91[AFR][1000 genomes]
rs892647	0.97[AFR][1000 genomes]
rs9721742	0.85[ASN][1000 genomes]
rs9792431	0.88[ASN][1000 genomes]
rs9792684	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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:98557400-98577200	Weak transcription	Pancreas	Pancrea
3	chr9:98564400-98568600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr9:98565000-98569400	Weak transcription	HUVEC	blood vessel
5	chr9:98567400-98568600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:98567400-98570800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:98568000-98571400	Enhancers	Ovary	ovary
8	chr9:98568400-98569000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:98568400-98569000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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