Variant report

Variant	rs895959
Chromosome Location	chr12:122320352-122320353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122319850..122323065-chr12:122324628..122326672,4	MCF-7	breast:
2	chr12:122319572..122322353-chr12:122324355..122326595,2	MCF-7	breast:
3	chr12:122233528..122236149-chr12:122319048..122321732,2	K562	blood:
4	chr12:122238851..122242892-chr12:122319516..122321765,3	MCF-7	breast:
5	chr12:122320221..122322912-chr12:122324691..122327698,3	K562	blood:

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000212694	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10770186	0.91[YRI][hapmap]
rs10840626	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840627	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11043222	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11043226	0.85[AMR][1000 genomes]
rs11502392	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1154510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1154513	0.87[EUR][1000 genomes]
rs1154515	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11614623	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168674	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1169077	0.82[CEU][hapmap]
rs1169085	0.82[CEU][hapmap]
rs1169093	0.82[CEU][hapmap]
rs1182927	0.82[CEU][hapmap]
rs1185260	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1667580	0.88[EUR][1000 genomes]
rs1667583	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1667584	0.87[EUR][1000 genomes]
rs1678951	0.87[EUR][1000 genomes]
rs1678967	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1678969	0.84[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs1720041	0.82[CEU][hapmap]
rs1720067	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1795963	0.80[CHB][hapmap]
rs1795967	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1947826	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2101017	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2230681	0.85[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];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247139	0.88[EUR][1000 genomes]
rs2247291	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2309274	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596137	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596144	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2620332	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2620340	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688412	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707075	0.86[ASN][1000 genomes]
rs4760099	0.85[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];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493519	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs6486782	0.91[YRI][hapmap]
rs6486794	0.82[CEU][hapmap]
rs693277	0.87[EUR][1000 genomes]
rs7314056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957207	0.91[CEU][hapmap]
rs7961103	0.91[CEU][hapmap]
rs830122	0.82[CEU][hapmap]
rs830124	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs830126	0.81[EUR][1000 genomes]
rs853758	1.00[CEU][hapmap]
rs895958	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9668191	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs895959	RNF10	cis	cerebellum	SCAN
rs895959	SETD1B	cis	parietal	SCAN
rs895959	CCDC62	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122311000-122320400	Weak transcription	K562	blood
2	chr12:122311800-122321000	Weak transcription	Right Atrium	heart
3	chr12:122312000-122322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:122314600-122320800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:122319400-122321000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:122320000-122321000	Enhancers	HepG2	liver
7	chr12:122320000-122321800	Enhancers	Liver	Liver

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