Variant report

Variant	rs12211580
Chromosome Location	chr6:73441990-73441991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10455268	1.00[CHB][hapmap]
rs10484913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10485213	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10498884	1.00[CHD][hapmap]
rs10943048	1.00[ASN][1000 genomes]
rs10943050	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10943051	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs10943055	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10943057	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10943058	1.00[ASN][1000 genomes]
rs11759937	1.00[ASN][1000 genomes]
rs12189933	1.00[CHB][hapmap]
rs12189974	1.00[ASN][1000 genomes]
rs12191039	1.00[ASN][1000 genomes]
rs12191216	1.00[ASN][1000 genomes]
rs12191848	1.00[ASN][1000 genomes]
rs12192751	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12195259	1.00[ASN][1000 genomes]
rs12197962	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12199549	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12200468	1.00[CHB][hapmap]
rs12200908	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201380	1.00[ASN][1000 genomes]
rs12204139	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12204989	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12205374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208053	1.00[CHB][hapmap]
rs12208907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12210850	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12212268	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212419	1.00[ASN][1000 genomes]
rs12212562	1.00[CHB][hapmap]
rs12212818	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12214894	1.00[CHB][hapmap]
rs12214895	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12215865	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12374630	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12374631	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17692715	1.00[CHB][hapmap]
rs17692874	1.00[CHB][hapmap]
rs17692898	1.00[CHB][hapmap]
rs17729195	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs17749408	1.00[CHB][hapmap]
rs17749420	1.00[CHB][hapmap]
rs17796704	1.00[ASN][1000 genomes]
rs1928153	1.00[ASN][1000 genomes]
rs62411986	1.00[ASN][1000 genomes]
rs62411990	1.00[ASN][1000 genomes]
rs6453591	1.00[CHB][hapmap]
rs6931918	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6935174	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs719830	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72935423	1.00[ASN][1000 genomes]
rs73753888	0.85[EUR][1000 genomes]
rs7748594	1.00[ASN][1000 genomes]
rs7768673	1.00[CHB][hapmap]
rs7772197	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7776215	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

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	nsv1023809	chr6:73157813-73477997	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv538303	chr6:73157813-73477997	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3347486	chr6:73283590-73445976	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv830689	chr6:73385557-73544404	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830690	chr6:73391428-73574304	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv970046	chr6:73438631-73444293	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12211580	KCNQ5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73437800-73455200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:73438400-73455400	Weak transcription	HMEC	breast
3	chr6:73438600-73443000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:73438600-73447800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:73441600-73442600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:73441800-73442200	Enhancers	GM12878-XiMat	blood
7	chr6:73441800-73442400	ZNF genes & repeats	Psoas Muscle	Psoas
8	chr6:73441800-73442600	Enhancers	Primary B cells from cord blood	blood
9	chr6:73441800-73443800	Enhancers	Primary B cells from peripheral blood	blood

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