Variant report

Variant	rs2761680
Chromosome Location	chr9:95182133-95182134
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95180874..95182571-chr9:95184247..95186990,2	MCF-7	breast:
2	chr9:95176367..95178140-chr9:95181429..95184023,2	K562	blood:
3	chr9:95179674..95182574-chr9:95182721..95184992,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127083	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10120210	1.00[YRI][hapmap]
rs10125510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058726	0.88[EUR][1000 genomes]
rs1058751	0.88[EUR][1000 genomes]
rs10733744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144933	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1152760	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1152761	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1152762	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1175737	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1175923	0.88[EUR][1000 genomes]
rs1175929	0.82[EUR][1000 genomes]
rs1175930	0.88[EUR][1000 genomes]
rs1175931	0.81[CEU][hapmap]
rs11787696	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11789578	0.91[EUR][1000 genomes]
rs11792542	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11793505	0.88[EUR][1000 genomes]
rs11794966	0.84[EUR][1000 genomes]
rs12555097	0.82[EUR][1000 genomes]
rs1536423	1.00[YRI][hapmap]
rs2084289	0.88[EUR][1000 genomes]
rs2131918	1.00[YRI][hapmap]
rs2295939	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2296665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs230223	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2398749	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280213	0.91[EUR][1000 genomes]
rs41280215	0.91[EUR][1000 genomes]
rs472163	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs4743866	0.81[CEU][hapmap]
rs4743867	0.88[EUR][1000 genomes]
rs4743868	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs4743871	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4744124	0.88[EUR][1000 genomes]
rs4744125	0.88[EUR][1000 genomes]
rs501814	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs556155	0.81[CEU][hapmap]
rs557066	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs55894730	0.91[EUR][1000 genomes]
rs56374228	0.91[EUR][1000 genomes]
rs6479421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042199	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895639	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs9409464	0.91[EUR][1000 genomes]
rs9409465	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs9409466	0.81[CEU][hapmap]
rs9409467	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409469	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9409659	0.91[EUR][1000 genomes]
rs9409660	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409661	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409662	0.89[EUR][1000 genomes]
rs9409665	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9409666	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs944949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886781	1.00[YRI][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	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1053205	chr9:95119195-95182612	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2761680	C9orf79	cis	parietal	SCAN
rs2761680	ANKRD19	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95169400-95183800	Weak transcription	Aorta	Aorta
2	chr9:95173200-95184600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:95173200-95188400	Weak transcription	Fetal Heart	heart
4	chr9:95173800-95183400	Weak transcription	Fetal Stomach	stomach
5	chr9:95173800-95183400	Weak transcription	Ovary	ovary
6	chr9:95179600-95183000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links