Variant report

Variant	rs7970007
Chromosome Location	chr12:122931150-122931151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122914575..122917314-chr12:122929160..122931843,2	MCF-7	breast:
2	chr12:122929603..122932468-chr12:122945246..122946778,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10161184	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs10161488	0.86[EUR][1000 genomes]
rs10744218	0.94[EUR][1000 genomes]
rs10744242	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs10773090	0.95[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.80[EUR][1000 genomes]
rs10773108	0.82[EUR][1000 genomes]
rs10773117	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs10773162	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10773230	0.81[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs10846714	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10846852	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846871	0.83[ASN][1000 genomes]
rs10846899	0.98[ASN][1000 genomes]
rs10846912	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846968	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs11057522	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs11057686	0.83[EUR][1000 genomes]
rs11057813	0.84[EUR][1000 genomes]
rs11057819	0.84[EUR][1000 genomes]
rs11058178	0.94[ASN][1000 genomes]
rs11058272	0.91[EUR][1000 genomes]
rs1129167	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs11503023	0.84[EUR][1000 genomes]
rs11610303	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11830957	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12314537	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12812332	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12817342	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs12818177	0.84[EUR][1000 genomes]
rs12829449	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1392142	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1532579	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1553178	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2341438	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3825096	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4356269	0.86[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4758657	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4758658	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4758660	0.81[CHB][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap]
rs4758664	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4758665	0.80[EUR][1000 genomes]
rs4758692	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs4758693	0.88[EUR][1000 genomes]
rs4758695	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs6416295	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6488947	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs6489014	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs6489051	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6489056	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs7134381	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7296680	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7298839	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7305360	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311573	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs7313121	0.81[EUR][1000 genomes]
rs7313284	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs7953204	0.81[ASN][1000 genomes]
rs7955241	0.84[ASN][1000 genomes]
rs7955513	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs7959550	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7961258	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs7964981	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7972832	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7973480	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974160	0.95[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap]
rs7975492	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7978119	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7978636	0.81[EUR][1000 genomes]
rs868181	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs9788228	0.90[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv973945	chr12:122923254-122958354	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7970007	CCDC62	cis	cerebellum	SCAN
rs7970007	DYNLL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122922800-122931200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:122922800-122931600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:122922800-122960400	Weak transcription	Right Atrium	heart
4	chr12:122930600-122931400	Enhancers	Placenta	Placenta
5	chr12:122930600-122931400	Enhancers	HepG2	liver
6	chr12:122931000-122931400	Flanking Active TSS	Hela-S3	cervix
7	chr12:122931000-122932000	Enhancers	K562	blood

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