Variant report

Variant	rs2117432
Chromosome Location	chr9:98560147-98560148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98555048..98557462-chr9:98559025..98561990,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10121403	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10481647	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739632	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10760675	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10818017	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10983622	0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10983692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10983739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10983773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004422	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12375861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12553442	0.83[ASN][1000 genomes]
rs1410783	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1928253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164156	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2770837	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3930253	0.83[AMR][1000 genomes]
rs583716	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs585223	0.84[AMR][1000 genomes]
rs591579	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs601916	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs615866	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs631273	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs643815	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6478984	0.89[EUR][1000 genomes]
rs6479036	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs676453	0.83[AMR][1000 genomes]
rs680468	0.83[AMR][1000 genomes]
rs680754	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs683829	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs689627	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs689749	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs689871	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689979	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs690222	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs690304	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs690335	0.83[ASN][1000 genomes]
rs690455	0.83[AMR][1000 genomes]
rs700963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7024710	0.83[AMR][1000 genomes]
rs7868559	0.84[AMR][1000 genomes]
rs7874897	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs816671	0.92[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs816676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs816681	0.97[ASN][1000 genomes]
rs913408	0.83[AMR][1000 genomes]
rs9409321	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9409322	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2117432	LINC00476	cis	lung	GTEx
rs2117432	LINC00476	cis	Adipose Subcutaneous	GTEx
rs2117432	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs2117432	LINC00476	cis	Artery Aorta	GTEx
rs2117432	LINC00476	cis	Nerve Tibial	GTEx

Chromatin state (count:6 , 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	chr9:98557400-98563600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr9:98557400-98577200	Weak transcription	Pancreas	Pancrea
4	chr9:98557600-98562600	Weak transcription	HUVEC	blood vessel
5	chr9:98559800-98560200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:98559800-98560200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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