Variant report

Variant	rs3894058
Chromosome Location	chr9:94950642-94950643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94906898..94908988-chr9:94950032..94952563,2	K562	blood:
2	chr9:94939871..94945930-chr9:94946587..94952427,7	K562	blood:
3	chr9:94949592..94951281-chr9:95003090..95005092,2	K562	blood:
4	chr9:94946143..94949635-chr9:94950432..94953895,3	K562	blood:
5	chr1:117475586..117478112-chr9:94949296..94951385,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CENPP-8	chr9:94950436-94950659	NONHSAT133180

Variant related genes	Relation type
ENSG00000238996	Chromatin interaction
ENSG00000225511	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1058726	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1058751	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1144933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1152760	0.82[ASN][1000 genomes]
rs1152761	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1152762	0.82[ASN][1000 genomes]
rs1175737	0.82[ASN][1000 genomes]
rs1175923	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1175930	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1175931	0.87[CEU][hapmap]
rs11787696	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11789578	0.81[ASN][1000 genomes]
rs11790257	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791931	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792542	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11793505	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11794966	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555097	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084289	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2295939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41280213	0.85[ASN][1000 genomes]
rs41280215	0.85[ASN][1000 genomes]
rs472163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs4743862	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743863	0.81[ASN][1000 genomes]
rs4743864	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743866	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs4743867	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743868	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs4743871	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4744123	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744124	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744125	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs501814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs556155	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs557066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs56110031	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308715	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895639	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs9409464	0.91[ASN][1000 genomes]
rs9409465	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9409466	0.87[CEU][hapmap]
rs9409467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9409469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs9409659	0.85[ASN][1000 genomes]
rs9409660	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9409661	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9409662	0.82[ASN][1000 genomes]
rs9409665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs9409666	0.86[ASN][1000 genomes]
rs944949	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3894058	C9orf79	cis	parietal	SCAN
rs3894058	ANKRD19	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94944800-94955800	Weak transcription	Right Atrium	heart
2	chr9:94949000-94951800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:94949800-94952800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:94950000-94951400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:94950400-94950800	Weak transcription	GM12878-XiMat	blood
6	chr9:94950600-94950800	Enhancers	NH-A	brain
7	chr9:94950600-94951400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr9:94950600-94951600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:94950600-94954400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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