Variant report

Variant	rs7848096
Chromosome Location	chr9:104497569-104497570
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10739814	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760802	0.83[EUR][1000 genomes]
rs10760806	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10760807	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12552239	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337698	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1361103	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2050640	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2067056	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2067057	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2184959	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3983721	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4278209	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4474083	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479063	0.83[EUR][1000 genomes]
rs7020375	0.81[EUR][1000 genomes]
rs7872456	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1046590	chr9:104450624-104848588	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1046614	chr9:104492314-104686326	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1054992	chr9:104494816-104771134	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3482600	chr9:104496270-104498449	Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3482595	chr9:104496552-104498337	Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3482598	chr9:104496593-104498320	Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3482599	chr9:104496602-104498298	Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3482597	chr9:104496621-104498276	Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3482601	chr9:104496701-104498219	Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv14432	chr9:104496753-104498220	Weak transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv614963	chr9:104496792-104498057	Weak transcription Active TSS Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
14	nsv614964	chr9:104496792-104498109	Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv614965	chr9:104496792-104498188	Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv614966	chr9:104496966-104498109	Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv614967	chr9:104496966-104498188	Weak transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv614968	chr9:104497076-104498188	Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv614969	chr9:104497135-104498188	Bivalent/Poised TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv614970	chr9:104497187-104498188	Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7848096	XPA	cis	parietal	SCAN
rs7848096	C9orf30	cis	parietal	SCAN
rs7848096	C9orf125	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104494200-104499600	Weak transcription	Liver	Liver

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