Variant report

Variant	rs12146904
Chromosome Location	chr13:52700470-52700471
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	chr13:52699126..52701652-chr13:52702989..52705135,2	K562	blood:

Variant related genes	Relation type
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1004576	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1055062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1060631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs1134727	0.99[ASN][1000 genomes]
rs11620583	0.86[CHB][hapmap]
rs12431310	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12560598	0.90[ASN][1000 genomes]
rs1571189	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1801243	0.91[CHB][hapmap]
rs1886538	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1886539	0.98[ASN][1000 genomes]
rs1886542	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886543	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];1.00[ASN][1000 genomes]
rs1886544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1886545	0.91[ASN][1000 genomes]
rs1886546	0.90[ASN][1000 genomes]
rs1886547	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1924611	0.86[CHB][hapmap]
rs2004866	0.91[CHB][hapmap]
rs2005182	0.97[ASN][1000 genomes]
rs2181891	0.91[CHB][hapmap]
rs2274202	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2277448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2296347	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.98[ASN][1000 genomes]
rs2296348	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2296349	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408544	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408546	0.94[ASN][1000 genomes]
rs2408547	0.95[ASN][1000 genomes]
rs2408548	0.95[ASN][1000 genomes]
rs2408550	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408551	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408552	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs2408554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.99[ASN][1000 genomes]
rs2408609	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2408611	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897964	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2897965	0.94[ASN][1000 genomes]
rs2897977	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3368	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3742289	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3742291	0.90[ASN][1000 genomes]
rs3783242	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.99[ASN][1000 genomes]
rs3818422	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.99[ASN][1000 genomes]
rs3825528	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4261421	0.94[ASN][1000 genomes]
rs4264295	0.94[ASN][1000 genomes]
rs4297592	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4497567	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs4941727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4943060	0.89[ASN][1000 genomes]
rs61958804	0.91[ASN][1000 genomes]
rs61958805	0.88[ASN][1000 genomes]
rs6561656	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6561658	0.86[CHB][hapmap]
rs6650384	0.95[ASN][1000 genomes]
rs6650385	0.95[ASN][1000 genomes]
rs66849828	0.94[ASN][1000 genomes]
rs7318287	0.94[ASN][1000 genomes]
rs7319784	0.88[ASN][1000 genomes]
rs7320252	0.95[ASN][1000 genomes]
rs7320429	0.95[ASN][1000 genomes]
rs732071	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs7320831	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7321120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs7321310	0.88[ASN][1000 genomes]
rs7321435	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs7324458	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs7327634	0.91[CHB][hapmap]
rs7332356	0.90[ASN][1000 genomes]
rs7338131	0.95[ASN][1000 genomes]
rs747781	0.91[CHB][hapmap]
rs755363	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7981904	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7991237	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7995946	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7998770	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.99[ASN][1000 genomes]
rs9316563	0.86[CHB][hapmap]
rs9526819	0.86[CHB][hapmap]
rs9526823	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9526825	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9526826	0.95[ASN][1000 genomes]
rs9526834	0.96[ASN][1000 genomes]
rs9526835	0.94[ASN][1000 genomes]
rs9526836	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9526837	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9526842	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9526843	0.98[ASN][1000 genomes]
rs9535812	0.91[CHB][hapmap]
rs9535822	0.86[CHB][hapmap]
rs9535825	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs9535826	0.86[CHB][hapmap]
rs9535832	0.91[CHB][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs9535836	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535845	0.95[ASN][1000 genomes]
rs9535851	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535853	0.90[ASN][1000 genomes]
rs9535856	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535858	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535861	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs9535862	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535866	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535867	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9535871	0.95[ASN][1000 genomes]
rs9535873	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs9535878	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535879	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535882	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535883	0.90[ASN][1000 genomes]
rs9535885	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9535887	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535888	0.85[ASN][1000 genomes]
rs9535889	0.92[ASN][1000 genomes]
rs9563089	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9568682	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs9568684	0.89[JPT][hapmap]
rs9568692	0.95[ASN][1000 genomes]
rs9568713	0.91[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12146904	CKAP2	cis	cerebellum	SCAN
rs12146904	VPS36	cis	cerebellum	SCAN
rs12146904	CKAP2	cis	parietal	SCAN
rs12146904	NEK3	cis	Muscle Skeletal	GTEx
rs12146904	NCRNA00282	cis	cerebellum	SCAN
rs12146904	NEK5	cis	cerebellum	SCAN
rs12146904	ALG11	cis	Muscle Skeletal	GTEx
rs12146904	ATP7B	cis	cerebellum	SCAN
rs12146904	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52694400-52701600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr13:52699000-52701800	Enhancers	K562	blood

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