Variant report

Variant	rs11759134
Chromosome Location	chr6:49681846-49681847
allele	G/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	chr6:49680497-49681864	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49656231..49658922-chr6:49681368..49683254,2	MCF-7	breast:

Variant related genes	Relation type
CRISP2	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10485288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10948520	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs10948526	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10948527	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11750952	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11751801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11752255	0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs11752738	0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs11755024	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11755294	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757339	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11758714	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];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11759060	0.86[CEU][hapmap]
rs11759109	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs12200099	1.00[CHD][hapmap]
rs12524346	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs12524703	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12524712	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12525576	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs12525910	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12526063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12526795	0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs12527781	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12528045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528363	1.00[CEU][hapmap]
rs12529681	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12530051	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13190702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13191333	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13192504	1.00[JPT][hapmap]
rs13193306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193433	1.00[CEU][hapmap]
rs13194498	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs13194730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13194782	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs13195635	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13196440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13197915	1.00[JPT][hapmap]
rs13197952	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs13198297	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13198350	0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs13198479	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13200858	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13201512	0.82[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs13205275	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13206923	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13207529	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs13207716	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13209352	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs13210122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13212279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13212816	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13213771	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs13215868	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs13216991	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13217101	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs13218753	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13218826	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13219640	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1366927	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1429600	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1538194	0.86[CEU][hapmap]
rs17572279	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2050867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2059940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2059941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2082061	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2115678	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2145366	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2518100	1.00[JPT][hapmap]
rs34029456	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35908480	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35962311	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715140	1.00[JPT][hapmap]
rs62413635	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458711	1.00[JPT][hapmap]
rs751744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7762249	1.00[ASW][hapmap]
rs9473672	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs996678	1.00[JPT][hapmap]

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	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11759134	C6orf141	cis	cerebellum	SCAN
rs11759134	MUT	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49681000-49682000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:49681000-49682000	Bivalent/Poised TSS	NHEK	skin
3	chr6:49681000-49682200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:49681200-49682000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:49681600-49682000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:49681800-49682000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr6:49681800-49694200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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