Variant report

Variant	rs35881035
Chromosome Location	chr15:45297886-45297887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45297458-45297945	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:45297669-45298003	GM12891	blood:	n/a	n/a
3	POLR2A	chr15:45297467-45298116	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:45297657-45298075	GM12891	blood:	n/a	n/a
5	POLR2A	chr15:45297433-45298133	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:45297561-45298044	GM12891	blood:	n/a	n/a
7	POLR2A	chr15:45297481-45297946	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:45297553-45298118	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNU1-78P	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070438	0.82[EUR][1000 genomes]
rs11070439	0.89[ASN][1000 genomes]
rs11635836	0.96[ASN][1000 genomes]
rs12591229	0.82[EUR][1000 genomes]
rs12902552	0.84[ASN][1000 genomes]
rs12902975	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903068	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916850	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16976876	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2055858	0.96[ASN][1000 genomes]
rs2217932	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34428536	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759890	0.95[ASN][1000 genomes]
rs3858900	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58751943	0.81[ASN][1000 genomes]
rs67352586	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71405285	0.84[ASN][1000 genomes]
rs71478352	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169807	0.83[ASN][1000 genomes]
rs72722052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8182070	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1040940	chr15:45105374-45300844	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1048317	chr15:45152371-45326205	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv904184	chr15:45248787-45314764	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35881035	RP11-109D20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs35881035	SORD	cis	Skin Sun Exposed Lower leg	GTEx
rs35881035	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45297200-45300400	Weak transcription	Liver	Liver
2	chr15:45297400-45300400	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links